[gmx-users] Re: gromacs QM/MM compilation with gaussian (Txema Mercero)
Txema Mercero
jm.mercero at ehu.es
Wed Feb 16 14:39:30 CET 2011
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