[gmx-users] Re: gromacs QM/MM compilation with gaussian (Txema Mercero)
Txema Mercero
jm.mercero at ehu.es
Thu Feb 17 09:40:50 CET 2011
On Wed, Feb 16, 2011 at 2:44 PM, Gerrit Groenhof <ggroenh at gwdg.de> wrote:
> What is your path to the gaussian executable?
GAUSS_EXE=/software/g03gromacs/g03
GAUSS_DIR=/software/g03gromacs/g03
In this directories are all gaussian l*.exe files.
DEVEL_DIR=/software/g03gromacs/g03/modlinks
Txema
>
> 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
>>>
>>>
>
>
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