[gmx-users] Selection of force fields
Dear Tsjerk, Thanks for your reply. I am interested to work with ganglioside GM1. In that case which ffG will be appropriate for me. Ms. Anindita Gayen C/O Dr. Chaitali Mukhopadhyay Senior Research Fellow Department of Chemistry University of Calcutta 92, A. P. C. Road Kolkata-700 009 India Explore and discover exciting holidays and getaways with Yahoo! India Travel http://in.travel.yahoo.com/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Selection of force fields
Hi Anindita, I was sort of afraid you might be dealing with glycosphingolipids. The Gromos force fields do not have properly behaving models for sphingolipids yet. I'm not sure whether other force fields do much better. There's some serious parameterization to do here. If you have experimenal data or can get experimental data for the behaviour using ester lipid analogues, you could do simulations with those, which offer better behaviour in silico. Cheers, Tsjerk On 5/20/09, ANINDITA GAYEN aninditaga...@yahoo.co.in wrote: Dear Tsjerk, Thanks for your reply. I am interested to work with ganglioside GM1. In that case which ffG will be appropriate for me. Ms. Anindita Gayen C/O Dr. Chaitali Mukhopadhyay Senior Research Fellow Department of Chemistry University of Calcutta 92, A. P. C. Road Kolkata-700 009 India Explore and discover exciting holidays and getaways with Yahoo! India Travel http://in.travel.yahoo.com/ -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gromacs on glacier.westgrid.ca
Hello Payman,
Westgrid (and Glacier) has several pages of doc on its website about
running Gromacs and compiling softwares. I used to run (my own
compilation of) Gromacs on Glacier and never had any particular problem.
You just have to make sure you compile it with the correct mpicc and
fftw libraries. You also have make sure that you source the appropriate
path to mdrun in your script and that your GMXLIB path is correctly set.
Hope that helps,
Nicolas
Payman Pirzadeh a écrit :
Hi Justin,
Following is the script I use. But remember several points:
1. I compiled the gmx with double precision and did not rename the code to
mpi. I kept whatever was produced with _d suffix.
2. I use the same script for other codes and they work (I am using other MD
code for special purposes and a QM code as well).
3. This script follows the guidelines of glacier as well. It is available
online at http://www.westgrid.ca/support/quickstart/glacier
#!/bin/bash
#PBS -S /bin/bash
# Torque script for running an MPI program pn on glacier
# 2005-05-26 DSP
# This presumes code compiled with the Intel compiler.
# For example:
# /global/software/mpich-1.2.5.2/ssh/bin/mpif90 pn.f -o pn
#PBS -N sixsite-test
#PBS -l walltime=240:00:00
#PBS -l nodes=2:ppn=2
#PBS -l qos=parallel
MPIRUN=/global/software/mpich-1.2.5.2/ssh/bin/mpirun
cd $PBS_O_WORKDIR
echo Current working directory is `pwd`
echo Node file: $PBS_NODEFILE :
echo -
cat $PBS_NODEFILE
echo -
NUM_PROCS=`/bin/awk 'END {print NR}' $PBS_NODEFILE`
echo Running on $NUM_PROCS processors.
echo Starting run at: `date`
${MPIRUN} -np $NUM_PROCS -machinefile $PBS_NODEFILE -path
./global/home/pirzadeh/gromacs-4.0.4/bin/mdrun_d -deffnm npttest
echo Job finished at: `date`
Payman
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Payman Pirzadeh
Sent: May 19, 2009 12:36 PM
To: 'Discussion list for GROMACS users'
Subject: RE: [gmx-users] gromacs on glacier.westgrid.ca
Dear Tsjerk,
Thanks for your e-mail. The message that cluster sends is:
Running on 4 processors.
Starting run at: Sat May 16 17:13:28 PDT 2009
Warning: Command line arguments for program should be given
after the program name. Assuming that
./global/home/pirzadeh/gromacs-4.0.4/bin/mdrun_d is a
command line argument for the program.
Warning: Command line arguments for program should be given
after the program name. Assuming that -s is a
command line argument for the program.
Warning: Command line arguments for program should be given
after the program name. Assuming that npttest is a
command line argument for the program.
Missing: program name
Program -path either does not exist, is not
executable, or is an erroneous argument to mpirun.
Job finished at: Sat May 16 17:13:28 PDT 2009
The message that GROMACS has in log file is:
Program mdrun, VERSION 3.3.1
Source code file: gmxfio.c, line: 706
Can not open file:
topol.tpr
This is while I have the topology file in the same folder.
Payman
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Tsjerk Wassenaar
Sent: May 19, 2009 12:25 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] gromacs on glacier.westgrid.ca
Hi Payman,
That is probably not the only grid facility on which Gromacs may be
run and it would be helpful if you could give specifications of it
(WMS software e.g.), which could give you more response. Also, it
would be helpful if you'd be able to give more information regarding
the output. Then you'd also have to ask the question whether your
problem is grid related or gromacs related. In the former case you'd
better consult support from the facility you're trying to use.
Cheers,
Tsjerk
On Tue, May 19, 2009 at 6:19 PM, Payman Pirzadeh ppirz...@ucalgary.ca
wrote:
Hi All,
Is there anyone who is running gromacs on glacier.westgrid.ca machine? If
yes, I will be appreciated if he/she can tell me how to run gmx on this
facility. I either get error messages which says either the executable or
the topology file can not be found.
Regards,
Payman
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Re: Hi: Re: [gmx-users] Hello: Forcefield and potentials for DNA-zinc finger complex
Hi Nehme, I've did simulations on TRAIL, which also contains a zinc-finger domain, involving three cysteines and a chloride ion. But it's not so simple. Luckily the exact parameters seemed not that vital, as the zinc apparently functions to keep the three subunits together and was in any case not directly related to the properties we were interested in. Still, I spent some time parameterizing it. For that I did quite a search of the available literature. You'll find some references in our 2008 Proteins paper. One of the most striking things is the still unresolved issue of the protonation state of zinc finger domains. Especially in the acidic environment around DNA, this may become an issue. It is why I have stayed away from zinc-finger domains lately, as they'd cost me too much work properly parameterizing them, even though our lab is doing experimental work on them and it would be interesting to complement that with MD. That's also why I mentioned to be interested in such parameters. Not in what you can readily calculate with QM or what you can get from automatic topology builders or even from literature, including my own. That doesn't solve the issue of the protonation state or overall charge of the complex. I won't trust any report on zinc-finger domain MD, unless it is shown to properly reproduce experimental properties, including what can be determined in relation to the protonation state. Cheers, Tsjerk On Wed, May 20, 2009 at 10:40 AM, Nehme El Hachem n...@aub.edu.lb wrote: Hi Tsjerk, I thank you for your help. Indeed, I am very new to GROMACS ( I have a Linux Red hat 9.0 and I do have some issues installing the software). If you are interested, please find a link: http://www.epress.com/w3jbio/vol2/harris2/harris.htm Molecular Dynamics Simulation Of The Estrogen Receptor Protein In Complex With A Non-Consensus Estrogen Response Element DNA Sequence In A 10 Angstrom Water Layer. I am trying to do some molecular dynamics on the oestrogen receptor DNA binding domain (PDB code: 1HCQ). I have InsightII with Discover3 and CHARMm but I am confused with the type of forcefield that I need. Furthermore, I have to add counterions to neutralize the system, so it seems complicated. I wanted to try GROMACS, because it has many forcfields (ex: ffAmber) for modeling this type of system. I appreciate your help, Nehme. -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] gromacs on glacier.westgrid.ca
Hi,
On Tue, 19 May 2009 14:23:07 -0600, Payman Pirzadeh wrote
Hi Justin,
Following is the script I use. But remember several points:
${MPIRUN} -np $NUM_PROCS -machinefile $PBS_NODEFILE -path
./global/home/pirzadeh/gromacs-4.0.4/bin/mdrun_d -deffnm npttest
You have a dot before /global/... Are you sure this is the rigth path?
Hope this helps,
Rui Rodrigues
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[gmx-users] Failing installation with --enable-mpi option
I tried to install Gromacs on my Core2Quad pc with the command ./configure --enable-mpi --disable-nice --program-suffix=_mpi it is showing the following error result: [sand...@bhanu gromacs-4.0.3]$ ./configure --enable-mpi --disable-nice --program -suffix=_mpi checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes /bin/sh: /home/sandaka/Desktop/all: No such file or directory configure: WARNING: `missing' script is too old or missing checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... gcc3 checking for mpxlc... no checking for mpicc... mpicc checking whether the MPI cc command works... yes checking for catamount... no checking how to run the C preprocessor... mpicc -E checking whether mpicc accepts -O3... yes checking whether mpicc accepts -funroll-all-loops... yes checking whether mpicc accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops... yes checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... no checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking whether byte ordering is bigendian... no checking for int... yes checking size of int... configure: error: cannot compute sizeof (int) See `config.log' for more details. Am attaching the config.log file herein. I've Openmpi and fftw already installed and in the path.. Couldn't understand what is the error! -- Never lose hope on the person you love they maybe the reason your heart aches today... but they are definitely the reason your heart beats : COPIED FROM GMAIL CUSTOM MSGS. This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. It was created by gromacs configure 4.0.3, which was generated by GNU Autoconf 2.61. Invocation command line was $ ./configure --enable-mpi --disable-nice --program-suffix=_mpi ## - ## ## Platform. ## ## - ## hostname = bhanu.prakash uname -m = i686 uname -r = 2.6.23.1-42.fc8 uname -s = Linux uname -v = #1 SMP Tue Oct 30 13:55:12 EDT 2007 /usr/bin/uname -p = unknown /bin/uname -X = unknown /bin/arch = i686 /usr/bin/arch -k = unknown /usr/convex/getsysinfo = unknown /usr/bin/hostinfo = unknown /bin/machine = unknown /usr/bin/oslevel = unknown /bin/universe = unknown PATH: /usr/lib/qt-3.3/bin PATH: /usr/kerberos/bin PATH: /usr/lib/ccache PATH: /usr/local/bin PATH: /usr/bin PATH: /bin PATH: /usr/X11R6/bin PATH: /home/sandaka/bin ## --- ## ## Core tests. ## ## --- ## configure:2087: checking build system type configure:2105: result: i686-pc-linux-gnu configure:2127: checking host system type configure:2142: result: i686-pc-linux-gnu configure:2180: checking for a BSD-compatible install configure:2236: result: /usr/bin/install -c configure:2247: checking whether build environment is sane configure:2290: result: yes configure:2314: WARNING: `missing' script is too old or missing configure:2318: checking for a thread-safe mkdir -p configure:2357: result: /bin/mkdir -p configure:2370: checking for gawk configure:2386: found /usr/bin/gawk configure:2397: result: gawk configure:2408: checking whether make sets $(MAKE) configure:2429: result: yes configure:2612: checking how to create a ustar tar archive configure:2625: tar --version tar (GNU tar) 1.17 Copyright (C) 2007 Free Software Foundation, Inc. License GPLv2+: GNU GPL version 2 or later http://gnu.org/licenses/gpl.html This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Written by John Gilmore and Jay Fenlason. configure:2628: $? = 0 configure:2668: tardir=conftest.dir eval tar --format=ustar -chf - $tardir conftest.tar configure:2671: $? = 0 configure:2675: tar -xf - conftest.tar configure:2678: $? = 0 configure:2691: result: gnutar configure:3297: checking for cc configure:3313: found /usr/lib/ccache/cc
Re: [gmx-users] Failing installation with --enable-mpi option
Bhanu wrote: I tried to install Gromacs on my Core2Quad pc with the command ./configure --enable-mpi --disable-nice --program-suffix=_mpi it is showing the following error result: [sand...@bhanu gromacs-4.0.3]$ ./configure --enable-mpi --disable-nice --program -suffix=_mpi checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes /bin/sh: /home/sandaka/Desktop/all: No such file or directory configure: WARNING: `missing' script is too old or missing checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... gcc3 checking for mpxlc... no checking for mpicc... mpicc checking whether the MPI cc command works... yes checking for catamount... no checking how to run the C preprocessor... mpicc -E checking whether mpicc accepts -O3... yes checking whether mpicc accepts -funroll-all-loops... yes checking whether mpicc accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops... yes checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... no checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking whether byte ordering is bigendian... no checking for int... yes checking size of int... configure: error: cannot compute sizeof (int) See `config.log' for more details. Am attaching the config.log file herein. I've Openmpi and fftw already installed and in the path.. Couldn't understand what is the error! Have a look at this thread: http://www.gromacs.org/pipermail/gmx-users/2008-November/037935.html -Justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Failing installation with --enable-mpi option
Thanks Justin, will try your suggestion.. 2009/5/20 Justin A. Lemkul jalem...@vt.edu: Bhanu wrote: I tried to install Gromacs on my Core2Quad pc with the command ./configure --enable-mpi --disable-nice --program-suffix=_mpi it is showing the following error result: [sand...@bhanu gromacs-4.0.3]$ ./configure --enable-mpi --disable-nice --program -suffix=_mpi checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes /bin/sh: /home/sandaka/Desktop/all: No such file or directory configure: WARNING: `missing' script is too old or missing checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... gcc3 checking for mpxlc... no checking for mpicc... mpicc checking whether the MPI cc command works... yes checking for catamount... no checking how to run the C preprocessor... mpicc -E checking whether mpicc accepts -O3... yes checking whether mpicc accepts -funroll-all-loops... yes checking whether mpicc accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops... yes checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... no checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking whether byte ordering is bigendian... no checking for int... yes checking size of int... configure: error: cannot compute sizeof (int) See `config.log' for more details. Am attaching the config.log file herein. I've Openmpi and fftw already installed and in the path.. Couldn't understand what is the error! Have a look at this thread: http://www.gromacs.org/pipermail/gmx-users/2008-November/037935.html -Justin ___ gmx-users mailing list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing list gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Never lose hope on the person you love they maybe the reason your heart aches today... but they are definitely the reason your heart beats : COPIED FROM GMAIL CUSTOM MSGS. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] autocorrelation functions from several simulations d
Hi all, I have some doubts regarding the general use of acfs. The molecule I am studying is formed by two polycyclic aromatic sub-units joined by a 20-alkene chain; it is something like this: /--\/--\ /--\/--\ A | | |-CH2-CH-CH2-CH-CH2(...)| | | B \--/\--/ \--/\--/ however the subunits are different (compared to the drawing above and one from the other) and contain heteroatoms. One of the subunits exist either in a reduced or oxydated state in organic solution (I have used DMSO and acetonitryle). In the reduced state the molecule forms hydrogen bonds between the subunits and can fold with subunit A bonded to B, while in the oxydated state these bonds do not exist and the subunits are free to move. Of course, to fold up starting from an open configuration the subunits must get close. I have several simulations of this system in the oxydated state. Starting from folded initial positions it eventually opens in all simulations. To follow the unfold process I have extracted the distance A-B (which I call Rab) from all simulations. When the H bonds exists Rab has small oscillations around a certain value while when it opens it can have any value up to the length of the molecule. It could make sense to calculate the acf of Rab (with g_analyze) from each simulation and use the autocorrelation time as an estimate of the unfold time? I think that, upon oxydation, the system becomes disordered (relative to Rab) and loose memory of past Rab values; the autocorrelation time should be shorter than that obtained for the reduced state. Since I have 10 simulations what is the correct way to average results? Calculate a mean autocorrelation time? Doing this yields an average t0 of 155 ps. If I define an average open Rab and closed Rab and the simply average the time to unfold i obtain 242+/-300 ps. Finally, should I use, instead of Rab the difference Rab-Rab0 where the Rab0 is the mean or median value (for each simulation)? greetings giordano ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Dihedral definition
Dear all, i have a simple question regarding definition of proper improper dihedral type in gromacs. As in ffgmxbon.itp. [ dihedraltypes ] ; j k func phi0 cp mult C OA 1 180.000 16.736 2 C N 1 180.000 33.472 2 [ dihedraltypes ] ; i l func q0 cq NR5* NR5 2 0.000 167.360 NR5* NR5* 2 0.000 167.360 where func=1 for proper func=2 for improper func=3 for R.B. Is for proper dihedral 2nd 3rd atom and for improper dihedral 1st last atom is considered? Ms. Anindita Gayen C/O Dr. Chaitali Mukhopadhyay Senior Research Fellow Department of Chemistry University of Calcutta 92, A. P. C. Road Kolkata-700 009 India Explore and discover exciting holidays and getaways with Yahoo! India Travel http://in.travel.yahoo.com/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Help with nitrile group in complx protein-ligand md
Hello I had a problem with mdrun while trying to run trajectories for protein ligand complexes. I`ve already done successful calculations with 60 complexes, unfortunately 4 complexes gave the following error. The entire output is too big to copy, so I have only copied the error part. But lots of numbers appear before this error. Program mdrun, VERSION 4.0.4 Source code file: constr.c, line: 136 Fatal error: Too many LINCS warnings (1522) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem --- These ligands all have in common the nitrile group linked to an aromatic ring. I am using the gromos 53a6 forcefield. The minimization step ran normally for these complexes, so I only had problems when I tried to run the md simulations. I have alreay tryed some of the solutions given by the gmx user`s list like subtituting LINCS for SHAKE. Maybe my error has something to do with the nitrile group. Has anyone had any problem like this before? I would like some help on the matter Jocley ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Help with nitrile group in complx protein-ligand md
Jocley Araujo wrote: Hello I had a problem with mdrun while trying to run trajectories for protein ligand complexes. I`ve already done successful calculations with 60 complexes, unfortunately 4 complexes gave the following error. The entire output is too big to copy, so I have only copied the error part. But lots of numbers appear before this error. Program mdrun, VERSION 4.0.4 Source code file: constr.c, line: 136 Fatal error: Too many LINCS warnings (1522) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem --- These ligands all have in common the nitrile group linked to an aromatic ring. I am using the gromos 53a6 forcefield. The minimization step ran normally for these complexes, so I only had problems when I tried to run the md simulations. I have alreay tryed some of the solutions given by the gmx user`s list like subtituting LINCS for SHAKE. Maybe my error has something to do with the nitrile group. Has anyone had any problem like this before? I would like some help on the matter You need to define a virtual site. If you have C1-C2#N3 you want to make a bond (constraint) between 1 and 3, and define 2 as a vsite (check manual). Jocley ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Help with nitrile group in complx protein-ligand md
Jocley Araujo wrote: Hello I had a problem with mdrun while trying to run trajectories for protein ligand complexes. I`ve already done successful calculations with 60 complexes, unfortunately 4 complexes gave the following error. The entire output is too big to copy, so I have only copied the error part. But lots of numbers appear before this error. Program mdrun, VERSION 4.0.4 Source code file: constr.c, line: 136 Fatal error: Too many LINCS warnings (1522) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem --- These ligands all have in common the nitrile group linked to an aromatic ring. I am using the gromos 53a6 forcefield. The minimization step ran normally for these complexes, so I only had problems when I tried to run the md simulations. I have alreay tryed some of the solutions given by the gmx user`s list like subtituting LINCS for SHAKE. Maybe my error has something to do with the nitrile group. Has anyone had any problem like this before? Something is physically unrealistic about your system, leading to LINCS crashing. Where did you get your parameters for the nitrile group? If this is the common thread for the systems that crash, you can bet that whatever parameters you are using are not reliable. -Justin I would like some help on the matter Jocley ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] pdb2gmx file error
Hi Justin I am trying to prep a pdb file for md but keep on getting this error message Fatal error: Chain identifier 'O' was used in two non-sequential blocks (residue 2400, atom 18726) Fatal error: But when I look at the file I only have one chain identifier. Also when I strip off hydrogens and run pdb2gmx again this is the error I get Fatal error: Atom CB not found in residue VAL20 while adding hydrogens I donot understand why and would appreciate some help Thanks Dadado --- En date de : Mer 20.5.09, Justin A. Lemkul jalem...@vt.edu a écrit : De: Justin A. Lemkul jalem...@vt.edu Objet: Re: [gmx-users] Failing installation with --enable-mpi option À: Discussion list for GROMACS users gmx-users@gromacs.org Date: Mercredi 20 Mai 2009, 14h01 Bhanu wrote: I tried to install Gromacs on my Core2Quad pc with the command ./configure --enable-mpi --disable-nice --program-suffix=_mpi it is showing the following error result: [sand...@bhanu gromacs-4.0.3]$ ./configure --enable-mpi --disable-nice --program -suffix=_mpi checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes /bin/sh: /home/sandaka/Desktop/all: No such file or directory configure: WARNING: `missing' script is too old or missing checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... gcc3 checking for mpxlc... no checking for mpicc... mpicc checking whether the MPI cc command works... yes checking for catamount... no checking how to run the C preprocessor... mpicc -E checking whether mpicc accepts -O3... yes checking whether mpicc accepts -funroll-all-loops... yes checking whether mpicc accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops... yes checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... no checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking whether byte ordering is bigendian... no checking for int... yes checking size of int... configure: error: cannot compute sizeof (int) See `config.log' for more details. Am attaching the config.log file herein. I've Openmpi and fftw already installed and in the path.. Couldn't understand what is the error! Have a look at this thread: http://www.gromacs.org/pipermail/gmx-users/2008-November/037935.html -Justin ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_clustsize method
It would be very advantageous for me to have a g_clustsize that could implement the Jarvis-Patrick method instead of single linkage. Would this be very difficult to achieve? Or would it be easy enough to use source code from g_cluster and do a sort of transplant? Thank you for you help David van der Spoel sp...@xray.bmc.uu.se 5/19/2009 10:06 PM Jacob Spooner wrote: I am planning on using g_clustsize to do some condensation analysis. I looked at g_cluster and see that it has a number of method options including single linkage and jarvis patrick. Is it true that g_clustsize has only the single linkage option? I took a look at the source code but this type of thing is not my strength. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Yes. Is that not sufficient? -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Dihedral definition
ANINDITA GAYEN wrote: Dear all, i have a simple question regarding definition of proper improper dihedral type in gromacs. As in ffgmxbon.itp please upgrade your force field. For most force fields there is a proper description but there is not for this one. Therefore we discourage people from using it. [ dihedraltypes ] ; jk func phi0 cp mult C OA1 180.000 16.736 2 CN1 180.000 33.472 2 [ dihedraltypes ] ; il funcq0 cq NR5* NR52 0.000 167.360 NR5* NR5*2 0.000 167.360 where func=1 for proper func=2 for improper func=3 for R.B. Is for proper dihedral 2^nd 3^rd atom and for improper dihedral 1^st last atom is considered? Ms. Anindita Gayen C/O Dr. Chaitali Mukhopadhyay Senior Research Fellow Department of Chemistry University of Calcutta 92, A. P. C. Road Kolkata-700 009 India Explore and discover exciting holidays and getaways with Yahoo! India Travel Click here! http://in.rd.yahoo.com/tagline_Travel_1/*http://in.travel.yahoo.com/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: pdb2gmx file error
Please keep all Gromacs-related correspondence on the gmx-users list; I do not advertise as a free tutor :) yimnai forlemu wrote: Hi Justin I am trying to prep a pdb file for md but keep on getting this error message Fatal error: Chain identifier 'O' was used in two non-sequential blocks (residue 2400, atom 18726) Fatal error: But when I look at the file I only have one chain identifier. Then something is either incorrectly formatted, or you are not finding the real problem. Look at the line pdb2gmx is pointing to, and see here: http://wiki.gromacs.org/index.php/Errors#Chain_identifier_.27X.27_was_used_in_two_non-sequential_blocks Also when I strip off hydrogens and run pdb2gmx again this is the error I get Fatal error: Atom CB not found in residue VAL20 while adding hydrogens You have a broken structure. Check the header of the .pdb file for MISSING entries. Also, refer here: http://wiki.gromacs.org/index.php/Errors#Long_bonds_and.2For_missing_atoms Most errors that new users face can be found in wiki entries, or by searching the list archive. -Justin I donot understand why and would appreciate some help Thanks Dadado --- En date de : *Mer 20.5.09, Justin A. Lemkul /jalem...@vt.edu/* a écrit : De: Justin A. Lemkul jalem...@vt.edu Objet: Re: [gmx-users] Failing installation with --enable-mpi option À: Discussion list for GROMACS users gmx-users@gromacs.org Date: Mercredi 20 Mai 2009, 14h01 Bhanu wrote: I tried to install Gromacs on my Core2Quad pc with the command ./configure --enable-mpi --disable-nice --program-suffix=_mpi it is showing the following error result: [sand...@bhanu gromacs-4.0.3]$ ./configure --enable-mpi --disable-nice --program -suffix=_mpi checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes /bin/sh: /home/sandaka/Desktop/all: No such file or directory configure: WARNING: `missing' script is too old or missing checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... gcc3 checking for mpxlc... no checking for mpicc... mpicc checking whether the MPI cc command works... yes checking for catamount... no checking how to run the C preprocessor... mpicc -E checking whether mpicc accepts -O3... yes checking whether mpicc accepts -funroll-all-loops... yes checking whether mpicc accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops... yes checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... no checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking whether byte ordering is bigendian... no checking for int... yes checking size of int... configure: error: cannot compute sizeof (int) See `config.log' for more details. Am attaching the config.log file herein. I've Openmpi and fftw already installed and in the path.. Couldn't understand what is the error! Have a look at this thread: http://www.gromacs.org/pipermail/gmx-users/2008-November/037935.html -Justin ___ gmx-users mailing listgmx-users@gromacs.org /mc/compose?to=gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org /mc/compose?to=gmx-users-requ...@gromacs.org. Can't post?
Re: [gmx-users] g_clustsize method
Jacob Spooner wrote: It would be very advantageous for me to have a g_clustsize that could implement the Jarvis-Patrick method instead of single linkage. Would this be very difficult to achieve? Or would it be easy enough to use source code from g_cluster and do a sort of transplant? Thank you for you help Maybe these two programs could be merged altogether, or at least the double code combined in a separate source file or so. Note that it is a good idea to check whether the algorithms have been implemented correctly anyway. David van der Spoel sp...@xray.bmc.uu.se 5/19/2009 10:06 PM Jacob Spooner wrote: I am planning on using g_clustsize to do some condensation analysis. I looked at g_cluster and see that it has a number of method options including single linkage and jarvis patrick. Is it true that g_clustsize has only the single linkage option? I took a look at the source code but this type of thing is not my strength. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Yes. Is that not sufficient? -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Lipids forming unsual bonds
Hi ALL, I am simulating a GPCR protein in a POPC bilayer. I have followed Justins' tutorial to set up the system, but have used POPC instead of DPPC. I have used the same parameters given in that tutorial. Till equilibration everything went well. But after releasing the protein in the production MD, the lipids are forming usual cross bonds (seen in the form of long straight lines). How can I avoid this? Any suggestion is welcome. Parameters used for MD: -- title = GPCR in POPC Production MD ; Run parameters integrator = md ; leap-frog integrator nsteps = 50 ; 2 * 50 = 1000 ps (1 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 1000 ; save coordinates every 2 ps nstvout = 1000 ; save velocities every 2 ps nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps ; Bond parameters continuation = yes ; Restarting after NPT constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = Nose-Hoover ; More accurate thermostat tc-grps = Protein POPC SOL_CL- ; three coupling groups - more accurate tau_t = 0.1 0.1 0.1 ; time constant, in ps ref_t = 323 323 323 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = semiisotropic ; uniform scaling of x-y box vectors, independent z tau_p = 2.0 ; time constant, in ps ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; Velocity generation is off --- Regards, Anirban GhoshGrade Based Engineer Bioinformatics Team Centre for Development of Advanced Computing (C-DAC) Pune, India Explore and discover exciting holidays and getaways with Yahoo! India Travel http://in.travel.yahoo.com/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Lipids forming unsual bonds
What exactly do you mean by unusual cross bonds? I suspect what you are seeing is simply a visualisation artifact, with a molecule being displayed across a PBC in the viewer you are using. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Lipids forming unsual bonds
Anirban Ghosh wrote: Hi ALL, I am simulating a GPCR protein in a POPC bilayer. I have followed Justins' tutorial to set up the system, but have used POPC instead of DPPC. I have used the same parameters given in that tutorial. Till equilibration everything went well. But after releasing the protein in the production MD, the lipids are forming usual cross bonds (seen in the form of long straight lines). How can I avoid this? Any suggestion is welcome. Bonds don't form in MD. Probably, the heuristic that your visualization software is using to guess where bonds exist isn't working the way you expected. I can't tell from your description, but you may being seeing bonds across the simulation box when the periodic boundaries intersect with molecules. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Lipids forming unsual bonds
the lipids are forming usual cross bonds (seen in the form of long straight lines) lines? on what? You need to do a much better job of describing your problem and your observations before anyone can give you a better suggestion than remove those lines and everything will be solved... That said, you're probably running into a regular pbc issue in vmd and you should then start with a .gro developed from trjconv -pbc mol or else you might try the dynamic bonds vmd representation. Otherwise, perhaps you are talking about loading in a post-equilibration .gro wherein the bond determination routine is finding bonds that don't make any sense and therefore your parameters or EM are probably bad. Still, a better description gets better assistance. Chris. -- original message -- Hi ALL, I am simulating a GPCR protein in a POPC bilayer. I have followed Justins' tutorial to set up the system, but have used POPC instead of DPPC. I have used the same parameters given in that tutorial. Till equilibration everything went well. But after releasing the protein in the production MD, the lipids are forming usual cross bonds (seen in the form of long straight lines). How can I avoid this? Any suggestion is welcome. Parameters used for MD: -- title= GPCR in POPC Production MD ; Run parameters integrator= md; leap-frog integrator nsteps= 50; 2 * 50 = 1000 ps (1 ns) dt= 0.002; 2 fs ; Output control nstxout= 1000; save coordinates every 2 ps nstvout= 1000; save velocities every 2 ps nstxtcout= 1000; xtc compressed trajectory output every 2 ps nstenergy= 1000; save energies every 2 ps nstlog= 1000; update log file every 2 ps ; Bond parameters continuation= yes; Restarting after NPT constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cels nstlist= 5; 10 fs rlist= 1.2; short-range neighborlist cutoff (in nm) rcoulomb= 1.2; short-range electrostatic cutoff (in nm) rvdw= 1.2; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT ; Temperature coupling is on tcoupl= Nose-Hoover; More accurate thermostat tc-grps= Protein POPCSOL_CL-; three coupling groups - more accurate tau_t= 0.10.10.1; time constant, in ps ref_t= 323 323323; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl= Parrinello-Rahman; Pressure coupling on in NPT pcoupltype= semiisotropic; uniform scaling of x-y box vectors, independent z tau_p= 2.0; time constant, in ps ref_p= 1.01.0; reference pressure, x-y, z (in bar) compressibility = 4.5e-54.5e-5; isothermal compressibility, bar^-1 ; Periodic boundary conditions pbc= xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel= no; Velocity generation is off --- Regards, Anirban GhoshGrade Based Engineer Bioinformatics Team Centre for Development of Advanced Computing (C-DAC) Pune, India Explore and discover exciting holidays and getaways with Yahoo! India Travel http://in.travel.yahoo.com/ -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20090521/320022c5/attachment.html -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
