[gmx-users] Re: gromacs QM/MM compilation with gaussian (Txema Mercero)

Gerrit Groenhof ggroenh at gwdg.de
Wed Feb 16 14:44:32 CET 2011


What is your path to the gaussian executable?

Gerrit
On 16 Feb 2011, at 14:39, Txema Mercero wrote:

> I get the same error which I attach this time:
> 
> 
> 
> -------------------------
> Back Off! I just backed up md.log to ./#md.log.8#
> Reading file topol.tpr, VERSION 4.5.3 (single precision)
> QM/MM calculation requested.
> there we go!
> Layer 0
> nr of QM atoms 24
> QMlevel: RHF/6-31G
> 
> number of CPUs for gaussian = 1
> memory for gaussian = 50000000
> accuracy in l510 = 8
> NOT using cp-mcscf in l1003
> Level of SA at start = 0
> /software/g03Gromacs/g03gaussian initialised...
> 
> Back Off! I just backed up traj.trr to ./#traj.trr.3#
> 
> Back Off! I just backed up ener.edr to ./#ener.edr.3#
> 
> Steepest Descents:
>   Tolerance (Fmax)   =  1.00000e+02
>   Number of steps    =         1000
> *** glibc detected ***
> /software/gromacs-4.5.3-shared-ifort11_gauss/bin/mdrun: malloc():
> memory corruption: 0x00000000077711b0 ***
> ======= Backtrace: =========
> /lib64/libc.so.6[0x3ddcc724ac]
> /lib64/libc.so.6(__libc_calloc+0xc0)[0x3ddcc73ce0]
> /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libgmx.so.6(save_calloc+0x32)[0x2b0e5ba08462]
> /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libmd.so.6(call_gaussian+0x81)[0x2b0e5b38cfd1]
> /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libmd.so.6(call_QMroutine+0x25)[0x2b0e5b384265]
> /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libmd.so.6(calculate_QMMM+0x665)[0x2b0e5b383bb5]
> /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libmd.so.6(do_force_lowlevel+0xd9)[0x2b0e5b2fcbd9]
> /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libmd.so.6(do_force+0xdaf)[0x2b0e5b35ae6f]
> /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libmd.so.6(do_steep+0x7d6)[0x2b0e5b314a26]
> /software/gromacs-4.5.3-shared-ifort11_gauss/bin/mdrun[0x4149ba]
> /software/gromacs-4.5.3-shared-ifort11_gauss/bin/mdrun[0x41dc03]
> /lib64/libc.so.6(__libc_start_main+0xf4)[0x3ddcc1d974]
> /software/gromacs-4.5.3-shared-ifort11_gauss/bin/mdrun(do_nm+0x4f1)[0x407069]
> ======= Memory map: ========
> 00400000-0046d000 r-xp 00000000 00:18 20054244
>  /software/gromacs-4.5.3-shared-ifort11_gauss/bin/mdrun
> 0066d000-00672000 rw-p 0006d000 00:18 20054244
>  /software/gromacs-4.5.3-shared-ifort11_gauss/bin/mdrun
> 00672000-00673000 rw-p 00672000 00:00 0
> 0770a000-077b6000 rw-p 0770a000 00:00 0                                  [heap]
> 3ddc800000-3ddc81c000 r-xp 00000000 08:02 5751044
>  /lib64/ld-2.5.so
> 3ddca1b000-3ddca1c000 r--p 0001b000 08:02 5751044
>  /lib64/ld-2.5.so
> 3ddca1c000-3ddca1d000 rw-p 0001c000 08:02 5751044
>  /lib64/ld-2.5.so
> 3ddcc00000-3ddcd4c000 r-xp 00000000 08:02 5750905
>  /lib64/libc-2.5.so
> 3ddcd4c000-3ddcf4c000 ---p 0014c000 08:02 5750905
>  /lib64/libc-2.5.so
> 3ddcf4c000-3ddcf50000 r--p 0014c000 08:02 5750905
>  /lib64/libc-2.5.so
> 3ddcf50000-3ddcf51000 rw-p 00150000 08:02 5750905
>  /lib64/libc-2.5.so
> 3ddcf51000-3ddcf56000 rw-p 3ddcf51000 00:00 0
> 3ddd000000-3ddd082000 r-xp 00000000 08:02 5750931
>  /lib64/libm-2.5.so
> 3ddd082000-3ddd281000 ---p 00082000 08:02 5750931
>  /lib64/libm-2.5.so
> 3ddd281000-3ddd282000 r--p 00081000 08:02 5750931
>  /lib64/libm-2.5.so
> 3ddd282000-3ddd283000 rw-p 00082000 08:02 5750931
>  /lib64/libm-2.5.so
> 3ddd400000-3ddd402000 r-xp 00000000 08:02 5750939
>  /lib64/libdl-2.5.so
> 3ddd402000-3ddd602000 ---p 00002000 08:02 5750939
>  /lib64/libdl-2.5.so
> 3ddd602000-3ddd603000 r--p 00002000 08:02 5750939
>  /lib64/libdl-2.5.so
> 3ddd603000-3ddd604000 rw-p 00003000 08:02 5750939
>  /lib64/libdl-2.5.so
> 3ddd800000-3ddd816000 r-xp 00000000 08:02 5751046
>  /lib64/libpthread-2.5.so
> 3ddd816000-3ddda15000 ---p 00016000 08:02 5751046
>  /lib64/libpthread-2.5.so
> 3ddda15000-3ddda16000 r--p 00015000 08:02 5751046
>  /lib64/libpthread-2.5.so
> 3ddda16000-3ddda17000 rw-p 00016000 08:02 5751046
>  /lib64/libpthread-2.5.so
> 3ddda17000-3ddda1b000 rw-p 3ddda17000 00:00 0
> 3dddc00000-3dddc14000 r-xp 00000000 08:02 10306767
>  /usr/lib64/libz.so.1.2.3
> 3dddc14000-3ddde13000 ---p 00014000 08:02 10306767
>  /usr/lib64/libz.so.1.2.3
> 3ddde13000-3ddde14000 rw-p 00013000 08:02 10306767
>  /usr/lib64/libz.so.1.2.3
> 3ddfc00000-3ddfc15000 r-xp 00000000 08:02 5751016
>  /lib64/libnsl-2.5.so
> 3ddfc15000-3ddfe14000 ---p 00015000 08:02 5751016
>  /lib64/libnsl-2.5.so
> 3ddfe14000-3ddfe15000 r--p 00014000 08:02 5751016
>  /lib64/libnsl-2.5.so
> 3ddfe15000-3ddfe16000 rw-p 00015000 08:02 5751016
>  /lib64/libnsl-2.5.so
> 3ddfe16000-3ddfe18000 rw-p 3ddfe16000 00:00 0
> 3de4400000-3de4533000 r-xp 00000000 08:02 10310609
>  /usr/lib64/libxml2.so.2.6.26
> 3de4533000-3de4733000 ---p 00133000 08:02 10310609
>  /usr/lib64/libxml2.so.2.6.26
> 3de4733000-3de473c000 rw-p 00133000 08:02 10310609
>  /usr/lib64/libxml2.so.2.6.26
> 3de473c000-3de473d000 rw-p 3de473c000 00:00 0
> 3dea200000-3dea20d000 r-xp 00000000 08:02 5751072
>  /lib64/libgcc_s-4.1.2-20080825.so.1
> 3dea20d000-3dea40d000 ---p 0000d000 08:02 5751072
>  /lib64/libgcc_s-4.1.2-20080825.so.1
> 3dea40d000-3dea40e000 rw-p 0000d000 08:02 5751072
>  /lib64/libgcc_s-4.1.2-20080825.so.1
> 2b0e5affe000-2b0e5b000000 rw-p 2b0e5affe000 00:00 0
> 2b0e5b000000-2b0e5b07e000 r-xp 00000000 00:18 20054237
>  /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libgmxpreprocess.so.6.0.0
> 2b0e5b07e000-2b0e5b27d000 ---p 0007e000 00:18 20054237
>  /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libgmxpreprocess.so.6.0.0
> 2b0e5b27d000-2b0e5b280000 rw-p 0007d000 00:18 20054237
>  /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libgmxpreprocess.so.6.0.0
> 2b0e5b280000-2b0e5b2ae000 rw-p 2b0e5b280000 00:00 0
> 2b0e5b2ae000-2b0e5b3b9000 r-xp 00000000 00:18 20054231
>  /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libmd.so.6.0.0
> 2b0e5b3b9000-2b0e5b5b9000 ---p 0010b000 00:18 20054231
>  /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libmd.so.6.0.0
> 2b0e5b5b9000-2b0e5b5bc000 rw-p 0010b000 00:18 20054231
>  /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libmd.so.6.0.0
> 2b0e5b5bc000-2b0e5b5bd000 rw-p 2b0e5b5bc000 00:00 0
> 2b0e5b5bd000-2b0e5b74c000 r-xp 00000000 00:18 49184804
>  /software/fftw-3.2.2_intel_11.0.069/lib/libfftw3f.so.3.2.4
> 2b0e5b74c000-2b0e5b94b000 ---p 0018f000 00:18 49184804
>  /software/fftw-3.2.2_intel_11.0.069/lib/libfftw3f.so.3.2.4
> 2b0e5b94b000-2b0e5b958000 rw-p 0018e000 00:18 49184804
>  /software/fftw-3.2.2_intel_11.0.069/lib/libfftw3f.so.3.2.4
> 2b0e5b958000-2b0e5b959000 rw-p 2b0e5b958000 00:00 0
> 2b0e5b96d000-2b0e5b96e000 rw-p 2b0e5b96d000 00:00 0
> 2b0e5b96e000-2b0e5bbbb000 r-xp 00000000 00:18 20054224
>  /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libgmx.so.6.0.0
> 2b0e5bbbb000-2b0e5bdbb000 ---p 0024d000 00:18 20054224
>  /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libgmx.so.6.0.0
> 2b0e5bdbb000-2b0e5bdcd000 rw-p 0024d000 00:18 20054224
>  /software/gromacs-4.5.3-shared-ifort11_gauss/lib/libgmx.so.6.0.0
> 2b0e5bdcd000-2b0e5bdce000 rw-p 2b0e5bdcd000 00:00 0
> 2b0e5bdce000-2b0e5c0b7000 r-xp 00000000 00:17 6031605
>  /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_intel_lp64.so
> 2b0e5c0b7000-2b0e5c1b6000 ---p 002e9000 00:17 6031605
>  /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_intel_lp64.so
> 2b0e5c1b6000-2b0e5c1c1000 rw-p 002e8000 00:17 6031605
>  /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_intel_lp64.so
> 2b0e5c1c1000-2b0e5c1c9000 rw-p 2b0e5c1c1000 00:00 0
> 2b0e5c1c9000-2b0e5c8c6000 r-xp 00000000 00:17 6031615
>  /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_sequential.so
> 2b0e5c8c6000-2b0e5c9c6000 ---p 006fd000 00:17 6031615
>  /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_sequential.so
> 2b0e5c9c6000-2b0e5c9d2000 rw-p 006fd000 00:17 6031615
>  /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_sequential.so
> 2b0e5c9d2000-2b0e5c9dd000 rw-p 2b0e5c9d2000 00:00 0
> 2b0e5c9dd000-2b0e5cc7a000 r-xp 00000000 00:17 6031599
>  /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.so
> 2b0e5cc7a000-2b0e5cd7a000 ---p 0029d000 00:17 6031599
>  /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.so
> 2b0e5cd7a000-2b0e5cd7f000 rw-p 0029d000 00:17 6031599
>  /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.so
> 2b0e5cd7f000-2b0e5cd92000 rw-p 2b0e5cd7f000 00:00 0
> 2b0e5cd92000-2b0e5cfe2000 r-xp 00000000 00:17 6783119
>  /opt/intel/Compiler/11.1/073/lib/intel64/libimf.so
> 2b0e5cfe2000-2b0e5d0e1000 ---p 00250000 00:17 6783119
>  /opt/intel/Compiler/11.1/073/lib/intel64/libimf.so
> 2b0e5d0e1000-2b0e5d126000 rw-p 0024f000 00:17 6783119
>  /opt/intel/Compiler/11.1/073/lib/intel64/libimf.so
> 2b0e5d126000-2b0e5d23c000 r-xp 00000000 00:17 6783139
>  /opt/intel/Compiler/11.1/073/lib/intel64/libsvml.so
> 2b0e5d23c000-2b0e5d33b000 ---p 00116000 00:17 6783139
>  /opt/intel/Compiler/11.1/073/lib/intel64/libsvml.so
> 2b0e5d33b000-2b0e5d33c000 rw-p 00115000 00:17 6783139
>  /opt/intel/Compiler/11.1/073/lib/intel64/libsvml.so
> 2b0e5d33c000-2b0e5d377000 r-xp 00000000 00:17 6783121
>  /opt/intel/Compiler/11.1/073/lib/intel64/libintlc.so.5
> 2b0e5d377000-2b0e5d476000 ---p 0003b000 00:17 6783121
>  /opt/intel/Compiler/11.1/073/lib/intel64/libintlc.so.5
> 2b0e5d476000-2b0e5d479000 rw-p 0003a000 00:17 6783121
>  /opt/intel/Compiler/11.1/073/lib/intel64/libintlc.so.5
> 2b0e5d479000-2b0e5d8b9000 rw-p 2b0e5d479000 00:00 0
> 2b0e60000000-2b0e60021000 rw-p 2b0e60000000 00:00 0
> 2b0e60021000-2b0e64000000 ---p 2b0e60021000 00:00 0
> 7fff4fa96000-7fff4faaa000 rwxp 7ffffffe9000 00:00 0                      [stack]
> 7fff4faaa000-7fff4faac000 rw-p 7fffffffd000 00:00 0
> ffffffffff600000-ffffffffffe00000 ---p 00000000 00:00 0                  [vdso]
> Aborted
> 
> 
> On Wed, Feb 16, 2011 at 2:08 PM, Gerrit Groenhof <ggroenh at gwdg.de> wrote:
>> 
>> Are you trying to run with more than one thread?
>> If so, try mdrun -nt 1
>> 
>> Gerrit
>> 
>>> 
>>>   1. Re: gromacs QM/MM compilation with gaussian (Txema Mercero)
>>>   2. Re: Periodic Boundary Conditions g_mindist -pi (ifat shub)
>>>   3. Re: Re: Periodic Boundary Conditions g_mindist -pi (Mark Abraham)
>>> 
>>> 
>>> ----------------------------------------------------------------------
>>> 
>>> Message: 1
>>> Date: Wed, 16 Feb 2011 12:23:49 +0100
>>> From: Txema Mercero <jm.mercero at ehu.es>
>>> Subject: [gmx-users] Re: gromacs QM/MM compilation with gaussian
>>> To: gmx-users at gromacs.org
>>> Cc: Edu Ogando <edu.ogando at ehu.es>, Jon I?aki Mujika
>>>       <joni.mujika at ehu.es>
>>> Message-ID:
>>>       <AANLkTi=O7w8CBEz90u-VzK+q+46EhH+RrTrtHgVUQ8Tz at mail.gmail.com>
>>> Content-Type: text/plain; charset=ISO-8859-1
>>> 
>>> Hi there!
>>> 
>>> We are trying to compile gromacs with Gaussian 03 rev D.02 (we also
>>> have g09). We followed the instructions in
>>> http://wwwuser.gwdg.de/~ggroenh/roadmap.pdf despite that they do no
>>> fit exactly  with the g03 rev d03 version,for instance, FrcNCN is no
>>> in l710 but in utilam.F
>>> 
>>> Despite of that, we compiled gromacs and  apparently everything was
>>> fine, but we get a segmentation fault when we run gromacs. We have the
>>> following questions
>>> 
>>> 1.- Is it possible to get a more detailed/or specific instructions?
>>> 2.- I think that three variables GAUSS_EXE, GAUSS_DIR and DEVEL_DIR
>>> should be defined. Where should GAUSS_EXE and GAUSS_DIR point exactly?
>>> 
>>> Thanks for your attention, any help will be appreciated.
>>> 
>>> Regards,
>>> 
>>> Txema Mercero
>>> IZO/SGI
>>> UPV/EHU
>>> 
>>> 
>>> ------------------------------
>>> 
>>> Message: 2
>>> Date: Wed, 16 Feb 2011 13:30:29 +0200
>>> From: ifat shub <shubifat at gmail.com>
>>> Subject: [gmx-users] Re: Periodic Boundary Conditions g_mindist -pi
>>> To: gmx-users at gromacs.org
>>> Message-ID:
>>>       <AANLkTi=71Moj0kH4=TR3_gDh54b1WsnEi0HUNDx++MQq at mail.gmail.com>
>>> Content-Type: text/plain; charset="iso-8859-1"
>>> 
>>> Hi Tsjerk,
>>> Thank you for your reply.
>>> I am aware of the trajconv option but I wanted to know if there is a way to
>>> avoid these kind of jumps over the periodic boundaries during the mdrun and
>>> not post process?
>>> Thanks,
>>> Ifat
>>> 
>>> message: 4
>>>> Date: Wed, 16 Feb 2011 11:19:14 +0200
>>>> From: ifat shub <shubifat at gmail.com>
>>>> Subject: [gmx-users] Periodic Boundary Conditions g_mindist -pi
>>>> To: gmx-users at gromacs.org
>>>> Message-ID:
>>>>       <AANLkTi=sgjfTmrf-0nVmZZOgfs+xhyxv5u6GGFNHR6hp at mail.gmail.com>
>>>> Content-Type: text/plain; charset="iso-8859-1"
>>>> 
>>>> Hi,
>>>> 
>>>> 
>>>> 
>>>> I am running a simulation on the complex 1aik.pdb in 310K. I wanted to see
>>>> if the complex is seeing its next periodic image, so I used the g_mindist
>>>> command with the -pi option. My command line was:
>>>> 
>>>> g_mindist -f run.xtc -s run.gro -n index.ndx -od tmp.xvg -pi
>>>> 
>>>> The output (see below) was stable until ~344ps when there is a  jump in the
>>>> max internal distance (third column) from ~6nm to ~22nm. After the jump the
>>>> numbers are reduced back to ~6nm and remained stable until the run is
>>>> completed at 1ns.
>>>> 
>>>> Does anyone know how to explain this jump? Is this a real problem or just a
>>>> visualization artifact? Is there a way to avoid such jumps?
>>>> 
>>>> 
>>>> 
>>>> Here is the mdp file I used:
>>>> 
>>>> ------run.mdp------
>>>> 
>>>> integrator      = md
>>>> 
>>>> nsteps          = 1000000
>>>> 
>>>> dt              = 0.001
>>>> 
>>>> coulombtype     = pme
>>>> 
>>>> vdw-type        = cut-off
>>>> 
>>>> tcoupl          = Berendsen
>>>> 
>>>> tc-grps         = protein non-protein
>>>> 
>>>> tau-t           = 0.1 0.1
>>>> 
>>>> ref-t           = 310 310
>>>> 
>>>> nstxout         = 100
>>>> 
>>>> nstvout         = 0
>>>> 
>>>> nstxtcout       = 100
>>>> 
>>>> nstenergy           = 100
>>>> 
>>>> comm_mode     = Linear ; Angular
>>>> 
>>>> comm_grps        = Protein
>>>> 
>>>> xtc_grps               = Protein
>>>> 
>>>> energygrps         = Protein
>>>> 
>>>> ------------------
>>>> 
>>>> 
>>>> 
>>>> Thanks,
>>>> 
>>>> Ifat
>>>> 
>>>> 
>>>> 
>>>> The output:
>>>> 
>>>> 343.7   10.813 5.924   16.445 16.445 16.445
>>>> 
>>>> 343.8   10.809 5.949   16.445 16.445 16.445
>>>> 
>>>> 343.9   10.804 5.959   16.445 16.445 16.445
>>>> 
>>>> 344      10.808 5.974   16.445 16.445 16.445
>>>> 
>>>> 344.1   0.18     21.982 16.445 16.445 16.445
>>>> 
>>>> 344.2   10.778 5.977   16.445 16.445 16.445
>>>> 
>>>> 344.3   10.768 5.996   16.445 16.445 16.445
>>>> 
>>>> 344.4   10.764 6.016   16.445 16.445 16.445
>>>> 
>>>> 344.5   10.722 6.029   16.445 16.445 16.445
>>>> 
>>>> 344.6   10.774 6.01     16.445 16.445 16.445
>>>> 
>>>> 344.7   0.174   21.984 16.445 16.445 16.445
>>>> 
>>>> 344.8   0.176   21.98   16.445 16.445 16.445
>>>> 
>>>> 344.9   0.17     22.002 16.445 16.445 16.445
>>>> 
>>>> 345      0.173   21.981 16.445 16.445 16.445
>>>> 
>>>> 345.1   0.191   21.954 16.445 16.445 16.445
>>>> 
>>>> 345.2   0.183   21.958 16.445 16.445 16.445
>>>> 
>>>> 345.3   0.181   22.012 16.445 16.445 16.445
>>>> 
>>>> 345.4   0.17     22.054 16.445 16.445 16.445
>>>> 
>>>> 345.5   0.168   22.054 16.445 16.445 16.445
>>>> 
>>>> 345.6   0.189   22.039 16.445 16.445 16.445
>>>> 
>>>> 345.7   0.171   22.007 16.445 16.445 16.445
>>>> 
>>>> 345.8   0.186   22.031 16.445 16.445 16.445
>>>> 
>>>> 345.9   0.171   22.077 16.445 16.445 16.445
>>>> 
>>>> 346      0.187   21.99   16.445 16.445 16.445
>>>> 
>>>> 346.1   0.173   21.984 16.445 16.445 16.445
>>>> 
>>>> 346.2   0.181   22.02   16.445 16.445 16.445
>>>> 
>>>> 346.3   10.82   5.984   16.445 16.445 16.445
>>>> 
>>>> 346.4   10.81   6.002   16.445 16.445 16.445
>>>> 
>>>> 346.5   10.819 6.008   16.445 16.445 16.445
>>>> 
>>>> 346.6   10.813 5.996   16.445 16.445 16.445
>>>> 
>>>> 346.7   10.781 6.006   16.445 16.445 16.445
>>>> 
>>>> 346.8   10.793 6.026   16.445 16.445 16.445
>>>> 
>>>> 346.9   10.745 5.985   16.445 16.445 16.445
>>>> 
>>>> 347      10.762 5.999   16.445 16.445 16.445
>>>> 
>>>> 347.1   10.781 5.984   16.445 16.445 16.445
>>>> 
>>>> 347.2   10.784 6.002   16.445 16.445 16.445
>>>> -------------- next part --------------
>>>> An HTML attachment was scrubbed...
>>>> URL:
>>>> http://lists.gromacs.org/pipermail/gmx-users/attachments/20110216/8495d798/attachment-0001.html
>>>> 
>>>> ------------------------------
>>>> 
>>>> Message: 5
>>>> Date: Wed, 16 Feb 2011 10:43:56 +0100
>>>> From: Tsjerk Wassenaar <tsjerkw at gmail.com>
>>>> Subject: Re: [gmx-users] Periodic Boundary Conditions g_mindist -pi
>>>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>>> Message-ID:
>>>>       <AANLkTinr05YyKV7rqzCSwEch=aBXFur+adKeNMxEMLEa at mail.gmail.com>
>>>> Content-Type: text/plain; charset=ISO-8859-1
>>>> 
>>>> Hi Ifat,
>>>> 
>>>> I guess this is a jump over the periodic boundaries. You should remove
>>>> jumps from the trajectory (-pbc nojump) before running g_mindist -pi.
>>>> 
>>>> Cheers,
>>>> 
>>>> Tsjerk
>>>> 
>>>> On Wed, Feb 16, 2011 at 10:19 AM, ifat shub <shubifat at gmail.com> wrote:
>>>>> Hi,
>>>>> 
>>>>> 
>>>>> 
>>>>> I am running a simulation on the complex 1aik.pdb in 310K. I wanted to
>>>> see
>>>>> if the complex is seeing its next periodic image, so I used the g_mindist
>>>>> command with the -pi option. My command line was:
>>>>> 
>>>>> g_mindist -f run.xtc -s run.gro -n index.ndx -od tmp.xvg -pi
>>>>> 
>>>>> The output (see below) was stable until ~344ps when there is a  jump in
>>>> the
>>>>> max internal distance (third column) from ~6nm to ~22nm. After the jump
>>>> the
>>>>> numbers are reduced back to ~6nm and remained stable until the run is
>>>>> completed at 1ns.
>>>>> 
>>>>> Does anyone know how to explain this jump? Is this a real problem or just
>>>> a
>>>>> visualization artifact? Is there a way to avoid such jumps?
>>>>> 
>>>>> 
>>>>> 
>>>>> Here is the mdp file I used:
>>>>> 
>>>>> ------run.mdp------
>>>>> 
>>>>> integrator      = md
>>>>> 
>>>>> nsteps          = 1000000
>>>>> 
>>>>> dt              = 0.001
>>>>> 
>>>>> coulombtype     = pme
>>>>> 
>>>>> vdw-type        = cut-off
>>>>> 
>>>>> tcoupl          = Berendsen
>>>>> 
>>>>> tc-grps         = protein non-protein
>>>>> 
>>>>> tau-t           = 0.1 0.1
>>>>> 
>>>>> ref-t           = 310 310
>>>>> 
>>>>> nstxout         = 100
>>>>> 
>>>>> nstvout         = 0
>>>>> 
>>>>> nstxtcout       = 100
>>>>> 
>>>>> nstenergy           = 100
>>>>> 
>>>>> comm_mode     = Linear ; Angular
>>>>> 
>>>>> comm_grps        = Protein
>>>>> 
>>>>> xtc_grps               = Protein
>>>>> 
>>>>> energygrps         = Protein
>>>>> 
>>>>> ------------------
>>>>> 
>>>>> 
>>>>> 
>>>>> Thanks,
>>>>> 
>>>>> Ifat
>>>>> 
>>>>> 
>>>>> 
>>>>> The output:
>>>>> 
>>>>> 343.7   10.813 5.924   16.445 16.445 16.445
>>>>> 
>>>>> 343.8   10.809 5.949   16.445 16.445 16.445
>>>>> 
>>>>> 343.9   10.804 5.959   16.445 16.445 16.445
>>>>> 
>>>>> 344      10.808 5.974   16.445 16.445 16.445
>>>>> 
>>>>> 344.1   0.18     21.982 16.445 16.445 16.445
>>>>> 
>>>>> 344.2   10.778 5.977   16.445 16.445 16.445
>>>>> 
>>>>> 344.3   10.768 5.996   16.445 16.445 16.445
>>>>> 
>>>>> 344.4   10.764 6.016   16.445 16.445 16.445
>>>>> 
>>>>> 344.5   10.722 6.029   16.445 16.445 16.445
>>>>> 
>>>>> 344.6   10.774 6.01     16.445 16.445 16.445
>>>>> 
>>>>> 344.7   0.174   21.984 16.445 16.445 16.445
>>>>> 
>>>>> 344.8   0.176   21.98   16.445 16.445 16.445
>>>>> 
>>>>> 344.9   0.17     22.002 16.445 16.445 16.445
>>>>> 
>>>>> 345      0.173   21.981 16.445 16.445 16.445
>>>>> 
>>>>> 345.1   0.191   21.954 16.445 16.445 16.445
>>>>> 
>>>>> 345.2   0.183   21.958 16.445 16.445 16.445
>>>>> 
>>>>> 345.3   0.181   22.012 16.445 16.445 16.445
>>>>> 
>>>>> 345.4   0.17     22.054 16.445 16.445 16.445
>>>>> 
>>>>> 345.5   0.168   22.054 16.445 16.445 16.445
>>>>> 
>>>>> 345.6   0.189   22.039 16.445 16.445 16.445
>>>>> 
>>>>> 345.7   0.171   22.007 16.445 16.445 16.445
>>>>> 
>>>>> 345.8   0.186   22.031 16.445 16.445 16.445
>>>>> 
>>>>> 345.9   0.171   22.077 16.445 16.445 16.445
>>>>> 
>>>>> 346      0.187   21.99   16.445 16.445 16.445
>>>>> 
>>>>> 346.1   0.173   21.984 16.445 16.445 16.445
>>>>> 
>>>>> 346.2   0.181   22.02   16.445 16.445 16.445
>>>>> 
>>>>> 346.3   10.82   5.984   16.445 16.445 16.445
>>>>> 
>>>>> 346.4   10.81   6.002   16.445 16.445 16.445
>>>>> 
>>>>> 346.5   10.819 6.008   16.445 16.445 16.445
>>>>> 
>>>>> 346.6   10.813 5.996   16.445 16.445 16.445
>>>>> 
>>>>> 346.7   10.781 6.006   16.445 16.445 16.445
>>>>> 
>>>>> 346.8   10.793 6.026   16.445 16.445 16.445
>>>>> 
>>>>> 346.9   10.745 5.985   16.445 16.445 16.445
>>>>> 
>>>>> 347      10.762 5.999   16.445 16.445 16.445
>>>>> 
>>>>> 347.1   10.781 5.984   16.445 16.445 16.445
>>>>> 
>>>>> 347.2   10.784 6.002   16.445 16.445 16.445
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> --
>>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>> Please search the archive at
>>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>>> Please don't post (un)subscribe requests to the list. Use the
>>>>> www interface or send it to gmx-users-request at gromacs.org.
>>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>> 
>>>> 
>>>> 
>>>> 
>>>> --
>>>> Tsjerk A. Wassenaar, Ph.D.
>>>> 
>>>> post-doctoral researcher
>>>> Molecular Dynamics Group
>>>> * Groningen Institute for Biomolecular Research and Biotechnology
>>>> * Zernike Institute for Advanced Materials
>>>> University of Groningen
>>>> The Netherlands
>>>> 
>>>> 
>>>> ------------------------------
>>>> 
>>>> --
>>>> gmx-users mailing list
>>>> gmx-users at gromacs.org
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>> Please search the archive at
>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>> 
>>>> End of gmx-users Digest, Vol 82, Issue 125
>>>> ******************************************
>>>> 
>>> -------------- next part --------------
>>> An HTML attachment was scrubbed...
>>> URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110216/daa11467/attachment-0001.html
>>> 
>>> ------------------------------
>>> 
>>> Message: 3
>>> Date: Wed, 16 Feb 2011 23:00:32 +1100
>>> From: Mark Abraham <Mark.Abraham at anu.edu.au>
>>> Subject: Re: [gmx-users] Re: Periodic Boundary Conditions g_mindist
>>>       -pi
>>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>> Message-ID: <4D5BBC60.5080600 at anu.edu.au>
>>> Content-Type: text/plain; charset="iso-8859-1"
>>> 
>>> On 16/02/2011 10:30 PM, ifat shub wrote:
>>>> 
>>>> Hi Tsjerk,
>>>> Thank you for your reply.
>>>> I am aware of the trajconv option but I wanted to know if there is a
>>>> way to avoid these kind of jumps over the periodic boundaries during
>>>> the mdrun and not post process?
>>> 
>>> No. mdrun does not know in advance what your visualization requirements
>>> are, and frankly there are better things to do with expensive compute
>>> cluster time. Post-processing a small number of frames elsewhere is much
>>> better use of resources.
>>> 
>>> Mark
>>> 
>>> 
>>>>    message: 4
>>>>    Date: Wed, 16 Feb 2011 11:19:14 +0200
>>>>    From: ifat shub <shubifat at gmail.com <mailto:shubifat at gmail.com>>
>>>>    Subject: [gmx-users] Periodic Boundary Conditions g_mindist -pi
>>>>    To: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>>>>    Message-ID:
>>>>    <AANLkTi=sgjfTmrf-0nVmZZOgfs+xhyxv5u6GGFNHR6hp at mail.gmail.com
>>>>    <mailto:sgjfTmrf-0nVmZZOgfs%2Bxhyxv5u6GGFNHR6hp at mail.gmail.com>>
>>>>    Content-Type: text/plain; charset="iso-8859-1"
>>>> 
>>>>    Hi,
>>>> 
>>>> 
>>>> 
>>>>    I am running a simulation on the complex 1aik.pdb in 310K. I
>>>>    wanted to see
>>>>    if the complex is seeing its next periodic image, so I used the
>>>>    g_mindist
>>>>    command with the -pi option. My command line was:
>>>> 
>>>>    g_mindist -f run.xtc -s run.gro -n index.ndx -od tmp.xvg -pi
>>>> 
>>>>    The output (see below) was stable until ~344ps when there is a
>>>>     jump in the
>>>>    max internal distance (third column) from ~6nm to ~22nm. After the
>>>>    jump the
>>>>    numbers are reduced back to ~6nm and remained stable until the run is
>>>>    completed at 1ns.
>>>> 
>>>>    Does anyone know how to explain this jump? Is this a real problem
>>>>    or just a
>>>>    visualization artifact? Is there a way to avoid such jumps?
>>>> 
>>>> 
>>>> 
>>>>    Here is the mdp file I used:
>>>> 
>>>>    ------run.mdp------
>>>> 
>>>>    integrator      = md
>>>> 
>>>>    nsteps          = 1000000
>>>> 
>>>>    dt              = 0.001
>>>> 
>>>>    coulombtype     = pme
>>>> 
>>>>    vdw-type        = cut-off
>>>> 
>>>>    tcoupl          = Berendsen
>>>> 
>>>>    tc-grps         = protein non-protein
>>>> 
>>>>    tau-t           = 0.1 0.1
>>>> 
>>>>    ref-t           = 310 310
>>>> 
>>>>    nstxout         = 100
>>>> 
>>>>    nstvout         = 0
>>>> 
>>>>    nstxtcout       = 100
>>>> 
>>>>    nstenergy           = 100
>>>> 
>>>>    comm_mode     = Linear ; Angular
>>>> 
>>>>    comm_grps        = Protein
>>>> 
>>>>    xtc_grps               = Protein
>>>> 
>>>>    energygrps         = Protein
>>>> 
>>>>    ------------------
>>>> 
>>>> 
>>>> 
>>>>    Thanks,
>>>> 
>>>>    Ifat
>>>> 
>>>> 
>>>> 
>>>>    The output:
>>>> 
>>>>    343.7   10.813 5.924   16.445 16.445 16.445
>>>> 
>>>>    343.8   10.809 5.949   16.445 16.445 16.445
>>>> 
>>>>    343.9   10.804 5.959   16.445 16.445 16.445
>>>> 
>>>>    344      10.808 5.974   16.445 16.445 16.445
>>>> 
>>>>    344.1   0.18     21.982 16.445 16.445 16.445
>>>> 
>>>>    344.2   10.778 5.977   16.445 16.445 16.445
>>>> 
>>>>    344.3   10.768 5.996   16.445 16.445 16.445
>>>> 
>>>>    344.4   10.764 6.016   16.445 16.445 16.445
>>>> 
>>>>    344.5   10.722 6.029   16.445 16.445 16.445
>>>> 
>>>>    344.6   10.774 6.01     16.445 16.445 16.445
>>>> 
>>>>    344.7   0.174   21.984 16.445 16.445 16.445
>>>> 
>>>>    344.8   0.176   21.98   16.445 16.445 16.445
>>>> 
>>>>    344.9   0.17     22.002 16.445 16.445 16.445
>>>> 
>>>>    345      0.173   21.981 16.445 16.445 16.445
>>>> 
>>>>    345.1   0.191   21.954 16.445 16.445 16.445
>>>> 
>>>>    345.2   0.183   21.958 16.445 16.445 16.445
>>>> 
>>>>    345.3   0.181   22.012 16.445 16.445 16.445
>>>> 
>>>>    345.4   0.17     22.054 16.445 16.445 16.445
>>>> 
>>>>    345.5   0.168   22.054 16.445 16.445 16.445
>>>> 
>>>>    345.6   0.189   22.039 16.445 16.445 16.445
>>>> 
>>>>    345.7   0.171   22.007 16.445 16.445 16.445
>>>> 
>>>>    345.8   0.186   22.031 16.445 16.445 16.445
>>>> 
>>>>    345.9   0.171   22.077 16.445 16.445 16.445
>>>> 
>>>>    346      0.187   21.99   16.445 16.445 16.445
>>>> 
>>>>    346.1   0.173   21.984 16.445 16.445 16.445
>>>> 
>>>>    346.2   0.181   22.02   16.445 16.445 16.445
>>>> 
>>>>    346.3   10.82   5.984   16.445 16.445 16.445
>>>> 
>>>>    346.4   10.81   6.002   16.445 16.445 16.445
>>>> 
>>>>    346.5   10.819 6.008   16.445 16.445 16.445
>>>> 
>>>>    346.6   10.813 5.996   16.445 16.445 16.445
>>>> 
>>>>    346.7   10.781 6.006   16.445 16.445 16.445
>>>> 
>>>>    346.8   10.793 6.026   16.445 16.445 16.445
>>>> 
>>>>    346.9   10.745 5.985   16.445 16.445 16.445
>>>> 
>>>>    347      10.762 5.999   16.445 16.445 16.445
>>>> 
>>>>    347.1   10.781 5.984   16.445 16.445 16.445
>>>> 
>>>>    347.2   10.784 6.002   16.445 16.445 16.445
>>>>    -------------- next part --------------
>>>>    An HTML attachment was scrubbed...
>>>>    URL:
>>>>    http://lists.gromacs.org/pipermail/gmx-users/attachments/20110216/8495d798/attachment-0001.html
>>>> 
>>>>    ------------------------------
>>>> 
>>>>    Message: 5
>>>>    Date: Wed, 16 Feb 2011 10:43:56 +0100
>>>>    From: Tsjerk Wassenaar <tsjerkw at gmail.com <mailto:tsjerkw at gmail.com>>
>>>>    Subject: Re: [gmx-users] Periodic Boundary Conditions g_mindist -pi
>>>>    To: Discussion list for GROMACS users <gmx-users at gromacs.org
>>>>    <mailto:gmx-users at gromacs.org>>
>>>>    Message-ID:
>>>>    <AANLkTinr05YyKV7rqzCSwEch=aBXFur+adKeNMxEMLEa at mail.gmail.com
>>>>    <mailto:aBXFur%2BadKeNMxEMLEa at mail.gmail.com>>
>>>>    Content-Type: text/plain; charset=ISO-8859-1
>>>> 
>>>>    Hi Ifat,
>>>> 
>>>>    I guess this is a jump over the periodic boundaries. You should remove
>>>>    jumps from the trajectory (-pbc nojump) before running g_mindist -pi.
>>>> 
>>>>    Cheers,
>>>> 
>>>>    Tsjerk
>>>> 
>>>>    On Wed, Feb 16, 2011 at 10:19 AM, ifat shub <shubifat at gmail.com
>>>>    <mailto:shubifat at gmail.com>> wrote:
>>>>> Hi,
>>>>> 
>>>>> 
>>>>> 
>>>>> I am running a simulation on the complex 1aik.pdb in 310K. I
>>>>    wanted to see
>>>>> if the complex is seeing its next periodic image, so I used the
>>>>    g_mindist
>>>>> command with the -pi option. My command line was:
>>>>> 
>>>>> g_mindist -f run.xtc -s run.gro -n index.ndx -od tmp.xvg -pi
>>>>> 
>>>>> The output (see below) was stable until ~344ps when there is a
>>>>     jump in the
>>>>> max internal distance (third column) from ~6nm to ~22nm. After
>>>>    the jump the
>>>>> numbers are reduced back to ~6nm and remained stable until the
>>>>    run is
>>>>> completed at 1ns.
>>>>> 
>>>>> Does anyone know how to explain this jump? Is this a real
>>>>    problem or just a
>>>>> visualization artifact? Is there a way to avoid such jumps?
>>>>> 
>>>>> 
>>>>> 
>>>>> Here is the mdp file I used:
>>>>> 
>>>>> ------run.mdp------
>>>>> 
>>>>> integrator      = md
>>>>> 
>>>>> nsteps          = 1000000
>>>>> 
>>>>> dt              = 0.001
>>>>> 
>>>>> coulombtype     = pme
>>>>> 
>>>>> vdw-type        = cut-off
>>>>> 
>>>>> tcoupl          = Berendsen
>>>>> 
>>>>> tc-grps         = protein non-protein
>>>>> 
>>>>> tau-t           = 0.1 0.1
>>>>> 
>>>>> ref-t           = 310 310
>>>>> 
>>>>> nstxout         = 100
>>>>> 
>>>>> nstvout         = 0
>>>>> 
>>>>> nstxtcout       = 100
>>>>> 
>>>>> nstenergy           = 100
>>>>> 
>>>>> comm_mode     = Linear ; Angular
>>>>> 
>>>>> comm_grps        = Protein
>>>>> 
>>>>> xtc_grps               = Protein
>>>>> 
>>>>> energygrps         = Protein
>>>>> 
>>>>> ------------------
>>>>> 
>>>>> 
>>>>> 
>>>>> Thanks,
>>>>> 
>>>>> Ifat
>>>>> 
>>>>> 
>>>>> 
>>>>> The output:
>>>>> 
>>>>> 343.7   10.813 5.924   16.445 16.445 16.445
>>>>> 
>>>>> 343.8   10.809 5.949   16.445 16.445 16.445
>>>>> 
>>>>> 343.9   10.804 5.959   16.445 16.445 16.445
>>>>> 
>>>>> 344      10.808 5.974   16.445 16.445 16.445
>>>>> 
>>>>> 344.1   0.18     21.982 16.445 16.445 16.445
>>>>> 
>>>>> 344.2   10.778 5.977   16.445 16.445 16.445
>>>>> 
>>>>> 344.3   10.768 5.996   16.445 16.445 16.445
>>>>> 
>>>>> 344.4   10.764 6.016   16.445 16.445 16.445
>>>>> 
>>>>> 344.5   10.722 6.029   16.445 16.445 16.445
>>>>> 
>>>>> 344.6   10.774 6.01     16.445 16.445 16.445
>>>>> 
>>>>> 344.7   0.174   21.984 16.445 16.445 16.445
>>>>> 
>>>>> 344.8   0.176   21.98   16.445 16.445 16.445
>>>>> 
>>>>> 344.9   0.17     22.002 16.445 16.445 16.445
>>>>> 
>>>>> 345      0.173   21.981 16.445 16.445 16.445
>>>>> 
>>>>> 345.1   0.191   21.954 16.445 16.445 16.445
>>>>> 
>>>>> 345.2   0.183   21.958 16.445 16.445 16.445
>>>>> 
>>>>> 345.3   0.181   22.012 16.445 16.445 16.445
>>>>> 
>>>>> 345.4   0.17     22.054 16.445 16.445 16.445
>>>>> 
>>>>> 345.5   0.168   22.054 16.445 16.445 16.445
>>>>> 
>>>>> 345.6   0.189   22.039 16.445 16.445 16.445
>>>>> 
>>>>> 345.7   0.171   22.007 16.445 16.445 16.445
>>>>> 
>>>>> 345.8   0.186   22.031 16.445 16.445 16.445
>>>>> 
>>>>> 345.9   0.171   22.077 16.445 16.445 16.445
>>>>> 
>>>>> 346      0.187   21.99   16.445 16.445 16.445
>>>>> 
>>>>> 346.1   0.173   21.984 16.445 16.445 16.445
>>>>> 
>>>>> 346.2   0.181   22.02   16.445 16.445 16.445
>>>>> 
>>>>> 346.3   10.82   5.984   16.445 16.445 16.445
>>>>> 
>>>>> 346.4   10.81   6.002   16.445 16.445 16.445
>>>>> 
>>>>> 346.5   10.819 6.008   16.445 16.445 16.445
>>>>> 
>>>>> 346.6   10.813 5.996   16.445 16.445 16.445
>>>>> 
>>>>> 346.7   10.781 6.006   16.445 16.445 16.445
>>>>> 
>>>>> 346.8   10.793 6.026   16.445 16.445 16.445
>>>>> 
>>>>> 346.9   10.745 5.985   16.445 16.445 16.445
>>>>> 
>>>>> 347      10.762 5.999   16.445 16.445 16.445
>>>>> 
>>>>> 347.1   10.781 5.984   16.445 16.445 16.445
>>>>> 
>>>>> 347.2   10.784 6.002   16.445 16.445 16.445
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> --
>>>>> gmx-users mailing list gmx-users at gromacs.org
>>>>    <mailto:gmx-users at gromacs.org>
>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>> Please search the archive at
>>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>>> Please don't post (un)subscribe requests to the list. Use the
>>>>> www interface or send it to gmx-users-request at gromacs.org
>>>>    <mailto:gmx-users-request at gromacs.org>.
>>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>> 
>>>> 
>>>> 
>>>> 
>>>>    --
>>>>    Tsjerk A. Wassenaar, Ph.D.
>>>> 
>>>>    post-doctoral researcher
>>>>    Molecular Dynamics Group
>>>>    * Groningen Institute for Biomolecular Research and Biotechnology
>>>>    * Zernike Institute for Advanced Materials
>>>>    University of Groningen
>>>>    The Netherlands
>>>> 
>>>> 
>>>>    ------------------------------
>>>> 
>>>>    --
>>>>    gmx-users mailing list
>>>>    gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>>>>    http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>    Please search the archive at
>>>>    http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>> 
>>>>    End of gmx-users Digest, Vol 82, Issue 125
>>>>    ******************************************
>>>> 
>>>> 
>>> 
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>>> ------------------------------
>>> 
>>> --
>>> gmx-users mailing list
>>> gmx-users at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> 
>>> End of gmx-users Digest, Vol 82, Issue 127
>>> ******************************************
>> 
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> 
>> 




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