[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
>>>> ******************************************
>>>>
>>>>
>>>
>>> -------------- next part --------------
>>> An HTML attachment was scrubbed...
>>> URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110216/1ab1794a/attachment.html
>>>
>>> ------------------------------
>>>
>>> --
>>> 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
>>
>>
More information about the gromacs.org_gmx-users
mailing list