[gmx-users] what do you do?
Dear All I want to know what project any Gromacs user is doing. In the other words what can we do by Gromacs. ** I am calculating binding free energy of drugs to their corresponding proteins ** Thanks in advance for your replies Mohsen -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Umberella sampling
Dear All I can't understand correctly what we do when we are using umberella sampling for obtaining PMF. I explain that ,please modify or complete it. (I think we define some sampling windows,each related to an reference distance. for each distance ,relative to it's distance,we define a spring constant. our spring is at rest in the center of windows, then we do a short simulation within each windows such that our molecule is connected to the spring and it's potential energy is depending to it's displacement from the center of windows. Then we have potential energy of two molecules in any distance from each other. Having potential energy along the reaction path or here falong the degree of freedom(distance between two molecules) is PMF oof interest and the difference between limits of PMF plot is delta-free energy of interest) what do you think ?do you agree with me? Thanks in advance for your atteintion. Mohsen -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g-WHAM
Dear All What is the algorithm of g-WHAM? in the other words ,what is the weighted histogeram analysis method? Thanks in advance for your reply Mohsen -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g-WHAM
Hi Mohsen, for a start, it is always a good idea to read the help text of a command you are interested in, or to check the most recent version of the manual. Using Gromacs 4.5 g_wham -h will guide you to a JCTC paper about g_wham, which is a nice starting point. Check out this paper as well as the references therein! Also Google is your friend here: http://pubs.acs.org/doi/abs/10.1021/ct100494z http://onlinelibrary.wiley.com/doi/10.1002/jcc.540130812/pdf Carsten On Dec 14, 2010, at 9:20 AM, mohsen ramezanpour wrote: Dear All What is the algorithm of g-WHAM? in the other words ,what is the weighted histogeram analysis method? Thanks in advance for your reply Mohsen -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] HBOND probability
Hello Justin,
I deleted the original file and re ran the script. I did get the output as
such:
#DonorAcceptor % Exist.
0.040
ASP1 N SOL171 OW 0.020
ASP1 N SOL172 OW 0.020
ASP1 N SOL175 OW 0.100
.
.
.
But in the second line of the output theres no donor or acceptor but still i
gives 0.040 % existence number. I scrolled down to end of the output file to
check if incase the %exist. is missing for the last atom...but everything
seems to be fine.
Please can i know why is it showing this number.
Kind regards,
chetan.
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: 13 December 2010 22:48
To: Gromacs Users' List
Subject: Re: [gmx-users] HBOND probability
Poojari, Chetan wrote:
Hello Justin,
I commented out line 151 and braces enclosing it.
# unless ($resn =~ /SOL/) {
for (my $z=1; $z=$nres; $z++) {
if ($donors{$z} == $natom) {
$donor_names[$z] = $name;
$donor_resn[$z] = join('', $resn, $resnum);
} elsif ($acceptors{$z} == $natom) {
$acceptor_names[$z] = $name;
$acceptor_resn[$z] = join('', $resn, $resnum);
}
}
# }
Following is the ouput:
In the beginning of the file i had these :
#Donor Acceptor % Exist.
0.040
ASP1 N 0.020
ASP1 N 0.020
ASP1 N 0.100
GLU11 OE1 0.020
GLU11 OE2 0.020
HIS13O
0.040
GLN15 OE1 0.040
Following these i had below lines., in the same file:
#Donor Acceptor % Exist.
0.040
ASP1 N SOL171 OW 0.020
ASP1 N SOL172 OW 0.020
ASP1 N SOL175 OW 0.100
ASP1 N SOL177 OW 0.020
ASP1 N SOL179 OW 0.020
.
.
.
.
SOL682OW HIS13 O
0.020
SOL682OW GLN15 OE1 0.020
SOL682OW GLN15 NE2 0.040
SOL682OW ALA21 O 0.020
SOL682OW GLU22 OE1 0.140
Delete the original file and run the script again. The output is simply
appended if the same file is already present. Or, modify the output routines.
The latter part of the file is the expected output.
-Justin
Kind regards,
chetan.
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: 13 December 2010 19:54
To: Gromacs Users' List
Subject: Re: [gmx-users] HBOND probability
Poojari, Chetan wrote:
Hello Justin,
I commented out the lines from 151-161
# unless ($resn =~ /SOL/) {
# for (my $z=1; $z=$nres; $z++) {
#if ($donors{$z} == $natom) {
#$donor_names[$z] = $name;
#$donor_resn[$z] = join('', $resn, $resnum);
# } elsif ($acceptors{$z} == $natom) {
# $acceptor_names[$z] = $name;
# $acceptor_resn[$z] = join('', $resn, $resnum);
# }
# }
# }
I am ending up with the similar output.
Please comment out *just* the unless line (151) and the brace that encloses
it,
not the entire section. Otherwise, I suspect that nothing actually happened.
That's the entire pattern matching operation there. Without it, the script
probably doesn't do anything at all.
-Justin
Kind regards,
chetan.
___
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On
Behalf Of Justin A. Lemkul [jalem...@vt.edu]
Sent: 13 December 2010 19:06
To: Gromacs Users' List
Subject: Re: [gmx-users] HBOND
[gmx-users] gmx-4.5.3 CMake build fails
Hello, building gromacs 4.5.3 with Cmake 2.6.3 fails because the build system cannot link g_analyze Linking C executable g_analyze ../gmxlib/libgmx.a(gmx_matrix.c.o): In function `matrix_invert': gmx_matrix.c:(.text+0x1d62): undefined reference to `dgetrf_' gmx_matrix.c:(.text+0x2442): undefined reference to `dgetri_' Note that I have GMX_EXTERNAL_BLAS -- ON GMX_EXTERNAL_LAPACK -- ON and the subsequently requested MKL_ settings have been properly inserted. I've tried to work around this by also adding the MKL libraries to CMAKE_EXE_LINKER_FLAGS, without avail. Any ideas? Regards Reinhold -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] ERROR: Source code file: statutil.c, line: 727
Hello madam, The command id *csh* *md.csh *As I see, there is no error in the command. All other commands are properly working (like eq.csh, em.csh etc ). The problem is only with md.csh. yours sincerely, uday. -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Coarse-grained simulation with MARTINI
On Dec 14, 2010, at 7:29, samio u940...@oz.nthu.edu.tw wrote: Hello I am trying to perform a CG simulation on the solvated protein but there is one question that I would like to ask for suggestion. The problem is: the volume of the periodic box varied a lot depending on the Van der Waals distance of the CG water molecule. I guess the volume variation is because of the system needs to relax to the correct density, since the number of water molecule is depending on the Van der Waals distance. Is it reasonable if I start the simulation after the volume become stable under position restraint? Yes it is. You may also want to tune the vdW radius you use in genbox to minimize the equilibration. More accurate the number, the quicker the equilibration. Thanks in advance for reading this post. -- Kuang-Yu Chang Institute of Bioinformatic and Structural Biology National Tsin Hua University 101, section 2, Kuang-Fu Road, Hsinchu 30013 Taiwan -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] ERROR: Source code file: statutil.c, line: 727
On Tue, Dec 14, 2010 at 10:07 AM, udaya kiran kiran.ud...@gmail.com wrote: Hello madam, The command id *csh* *md.csh * Please paste your md.csh file and the error you get in detail. **As I see, there is no error in the command. All other commands are properly working (like eq.csh, em.csh etc ). The problem is only with md.csh. yours sincerely, uday. -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists Best Wishes, Sarath -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] ERROR: Source code file: statutil.c, line: 727
Hello, Here I am sending the complete output after the md.csh command with the errors in bold. COMMAND: csh md.csh :-) G R O M A C S (-: Groningen Machine for Chemical Simulation :-) VERSION 4.0.5 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp (double precision) (-: Option Filename Type Description -f md-md.mdp Input, Opt! grompp input file with MD parameters -po inmd.mdp Output grompp input file with MD parameters -c results/eq1bar300K.gro InputStructure file: gro g96 pdb tpr tpb tpa -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -n Index_sol.ndx Input, Opt! Index file -p topol_sol_hbond_131210.top InputTopology file -pp processed.top Output, Opt. Topology file -o inmd.tpr Output Run input file: tpr tpb tpa -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt -e ener.edr Input, Opt. Energy file: edr ene Option Type Value Description -- -[no]h bool no Print help info and quit -niceint0 Set the nicelevel -[no]v bool yes Be loud and noisy -timereal -1 Take frame at or first after this time. -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -maxwarn int0 Number of allowed warnings during input processing -[no]zerobool no Set parameters for bonded interactions without defaults to zero instead of generating an error -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes *ERROR --- Program grompp, VERSION 4.0.5 Source code file: statutil.c, line: 727 Invalid command line argument: ---* Thanx for Using GROMACS - Have a Nice Day [1] 16658 : Command not found. :-) G R O M A C S (-: Great Red Oystrich Makes All Chemists Sane :-) VERSION 4.0.5 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) mdrun (double precision) (-: achje05 (/loch/akbl1/marelli/PROJECTS/16L4_16_aAALAA/16L4_GROMACS_RUN_HB3_131210) Option Filename Type Description -s inmd.tpr InputRun input file: tpr tpb tpa -o MDResults/md.trr Output Full precision trajectory: trr trj cpt -x MDResults/md.xtc Output, Opt. Compressed trajectory (portable xdr format) -cpi MDResults/md.cpt Input, Opt. Checkpoint file -cpo MDResults/md.cpt Output, Opt. Checkpoint file -c MDResults/md.gro Output Structure file: gro g96 pdb -e MDResults/md.edr Output Energy file: edr ene -g MDResults/md.log Output Log file -dgdl MDResults/md.xvg Output, Opt. xvgr/xmgr file -field MDResults/md.xvg Output, Opt. xvgr/xmgr file -table MDResults/md.xvg Input, Opt. xvgr/xmgr file -tablep MDResults/md.xvg Input, Opt. xvgr/xmgr file -tableb MDResults/md.xvg Input, Opt. xvgr/xmgr file -rerun MDResults/md.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt -tpi MDResults/md.xvg Output, Opt. xvgr/xmgr file -tpid MDResults/md.xvg Output, Opt. xvgr/xmgr file -ei MDResults/md.edi Input, Opt. ED sampling input -eo MDResults/md.edo Output, Opt. ED sampling output -j MDResults/md.gct Input, Opt. General coupling stuff -jo MDResults/md.gct Output, Opt.
Re: [gmx-users] ERROR: Source code file: statutil.c, line: 727
The input to your grompp command is wrong. You have selected an invalid grompp option. Please verify the grompp command and rerun the script. On Tue, Dec 14, 2010 at 11:13 AM, udaya kiran kiran.ud...@gmail.com wrote: Hello, Here I am sending the complete output after the md.csh command with the errors in bold. COMMAND: csh md.csh :-) G R O M A C S (-: Groningen Machine for Chemical Simulation :-) VERSION 4.0.5 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp (double precision) (-: Option Filename Type Description -f md-md.mdp Input, Opt! grompp input file with MD parameters -po inmd.mdp Output grompp input file with MD parameters -c results/eq1bar300K.gro InputStructure file: gro g96 pdb tpr tpb tpa -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -n Index_sol.ndx Input, Opt! Index file -p topol_sol_hbond_131210.top InputTopology file -pp processed.top Output, Opt. Topology file -o inmd.tpr Output Run input file: tpr tpb tpa -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt -e ener.edr Input, Opt. Energy file: edr ene Option Type Value Description -- -[no]h bool no Print help info and quit -niceint0 Set the nicelevel -[no]v bool yes Be loud and noisy -timereal -1 Take frame at or first after this time. -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -maxwarn int0 Number of allowed warnings during input processing -[no]zerobool no Set parameters for bonded interactions without defaults to zero instead of generating an error -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes *ERROR --- Program grompp, VERSION 4.0.5 Source code file: statutil.c, line: 727 Invalid command line argument: ---* Thanx for Using GROMACS - Have a Nice Day [1] 16658 : Command not found. :-) G R O M A C S (-: Great Red Oystrich Makes All Chemists Sane :-) VERSION 4.0.5 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) mdrun (double precision) (-: achje05 (/loch/akbl1/marelli/PROJECTS/16L4_16_aAALAA/16L4_GROMACS_RUN_HB3_131210) Option Filename Type Description -s inmd.tpr InputRun input file: tpr tpb tpa -o MDResults/md.trr Output Full precision trajectory: trr trj cpt -x MDResults/md.xtc Output, Opt. Compressed trajectory (portable xdr format) -cpi MDResults/md.cpt Input, Opt. Checkpoint file -cpo MDResults/md.cpt Output, Opt. Checkpoint file -c MDResults/md.gro Output Structure file: gro g96 pdb -e MDResults/md.edr Output Energy file: edr ene -g MDResults/md.log Output Log file -dgdl MDResults/md.xvg Output, Opt. xvgr/xmgr file -field MDResults/md.xvg Output, Opt. xvgr/xmgr file -table MDResults/md.xvg Input, Opt. xvgr/xmgr file -tablep MDResults/md.xvg Input, Opt. xvgr/xmgr file -tableb MDResults/md.xvg Input, Opt. xvgr/xmgr file -rerun MDResults/md.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt -tpi
Re: [gmx-users] ERROR: Source code file: statutil.c, line: 727
Hey there, just a guess into the blue... did you write that md.csh script yourself? It very much seems like that script is broken badly (see grompp output). Use your favorite text editor, open md.csh and paste it's content here. best, timo On 12/14/2010 11:13 AM, udaya kiran wrote: Hello, Here I am sending the complete output after the md.csh command with the errors in bold. COMMAND: csh md.csh :-) G R O M A C S (-: Groningen Machine for Chemical Simulation :-) VERSION 4.0.5 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp (double precision) (-: Option Filename Type Description -f md-md.mdp Input, Opt! grompp input file with MD parameters -po inmd.mdp Output grompp input file with MD parameters -c results/eq1bar300K.gro InputStructure file: gro g96 pdb tpr tpb tpa -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -n Index_sol.ndx Input, Opt! Index file -p topol_sol_hbond_131210.top InputTopology file -pp processed.top Output, Opt. Topology file -o inmd.tpr Output Run input file: tpr tpb tpa -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt -e ener.edr Input, Opt. Energy file: edr ene Option Type Value Description -- -[no]h bool no Print help info and quit -niceint0 Set the nicelevel -[no]v bool yes Be loud and noisy -timereal -1 Take frame at or first after this time. -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -maxwarn int0 Number of allowed warnings during input processing -[no]zerobool no Set parameters for bonded interactions without defaults to zero instead of generating an error -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes *ERROR --- Program grompp, VERSION 4.0.5 Source code file: statutil.c, line: 727 Invalid command line argument: ---* Thanx for Using GROMACS - Have a Nice Day [1] 16658 : Command not found. :-) G R O M A C S (-: Great Red Oystrich Makes All Chemists Sane :-) VERSION 4.0.5 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) mdrun (double precision) (-: achje05 (/loch/akbl1/marelli/PROJECTS/16L4_16_aAALAA/16L4_GROMACS_RUN_HB3_131210) Option Filename Type Description -s inmd.tpr InputRun input file: tpr tpb tpa -o MDResults/md.trr Output Full precision trajectory: trr trj cpt -x MDResults/md.xtc Output, Opt. Compressed trajectory (portable xdr format) -cpi MDResults/md.cpt Input, Opt. Checkpoint file -cpo MDResults/md.cpt Output, Opt. Checkpoint file -c MDResults/md.gro Output Structure file: gro g96 pdb -e MDResults/md.edr Output Energy file: edr ene -g MDResults/md.log Output Log file -dgdl MDResults/md.xvg Output, Opt. xvgr/xmgr file -field MDResults/md.xvg Output, Opt. xvgr/xmgr file -table MDResults/md.xvg Input, Opt. xvgr/xmgr file -tablep MDResults/md.xvg Input, Opt. xvgr/xmgr file -tableb MDResults/md.xvg Input, Opt. xvgr/xmgr file -rerun MDResults/md.xtc Input, Opt. Trajectory: xtc
[gmx-users] How to define Center of Mass velocity of a specific group
Dear all I have a system consisting of 2 substrates (20 nm distance between them) and inside them there are polymer chains. I would like during my NVT simulations the substrates NOT to move (I suppose I have to put the velocity of the COM of it's substrate to be zero). Does anyone know how to do that? Thanks in advance Chrysostomos -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Terminal_ARG_residue causing problem in pdb2gmx
On 14/12/2010 6:35 PM, shahid nayeem wrote: Dear Gromacs User My pdb is homodimer with Arg as c-terminal residue. With this pdb I am etting following error in pdb2gmx command Program pdb2gmx, VERSION 4.0.7 Source code file: pdb2gmx.c, line: 429 Fatal error: Atom OXT in residue ARG 107 not found in rtp entry with 17 atoms while sorting atoms The command executed is as follows pdb2gmx -f.pdb -o.gro -p .top I tried to change the OXT atom name in pdb file to O2, then also I am getting the same error. In .rtp entry there is ARG residue as N-ter but for C-ter ARG there is no residue. Please suggest. Waiting for helps from gromacs users. Shahid Nayem There have been problems with terminal oxygen atoms. Please upgrade to 4.5.3 and see if you still have problems. Mark -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How to define Center of Mass velocity of a specific group
Tomy van Batis wrote: Dear all I have a system consisting of 2 substrates (20 nm distance between them) and inside them there are polymer chains. I would like during my NVT simulations the substrates NOT to move (I suppose I have to put the velocity of the COM of it's substrate to be zero). Does anyone know how to do that? The simplest way is to just use position restraints. The positions may change very slightly, but not a noticeable amount. If you absolutely require no movement at all, use freezegrps in the .mdp file. -Justin Thanks in advance Chrysostomos -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] HBOND probability
Poojari, Chetan wrote:
Hello Justin,
I deleted the original file and re ran the script. I did get the output as such:
#DonorAcceptor % Exist.
0.040
ASP1 N SOL171 OW 0.020
ASP1 N SOL172 OW 0.020
ASP1 N SOL175 OW 0.100
.
.
.
But in the second line of the output theres no donor or acceptor but still i
gives 0.040 % existence number. I scrolled down to end of the output file to
check if incase the %exist. is missing for the last atom...but everything
seems to be fine.
Please can i know why is it showing this number.
I have no idea. There is some mismatch between the lines of the .xpm file and
the .ndx file, or for some reason the numbers in the .ndx file cannot be mapped
back onto the .pdb file. It could mean that this particular hydrogen bond is
undefined for those reasons, or something else later in the output file (since
the .xpm file is read backward, so to speak) has caused a problem and shifted
the indices.
If you send me your input files (off-list), I will try to find out what's going
on with them. No promises, but I'll try to find some time.
-Justin
Kind regards,
chetan.
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: 13 December 2010 22:48
To: Gromacs Users' List
Subject: Re: [gmx-users] HBOND probability
Poojari, Chetan wrote:
Hello Justin,
I commented out line 151 and braces enclosing it.
# unless ($resn =~ /SOL/) {
for (my $z=1; $z=$nres; $z++) {
if ($donors{$z} == $natom) {
$donor_names[$z] = $name;
$donor_resn[$z] = join('', $resn, $resnum);
} elsif ($acceptors{$z} == $natom) {
$acceptor_names[$z] = $name;
$acceptor_resn[$z] = join('', $resn, $resnum);
}
}
# }
Following is the ouput:
In the beginning of the file i had these :
#Donor Acceptor % Exist.
0.040
ASP1 N 0.020
ASP1 N 0.020
ASP1 N 0.100
GLU11 OE1 0.020
GLU11 OE2 0.020
HIS13O 0.040
GLN15 OE1 0.040
Following these i had below lines., in the same file:
#Donor Acceptor % Exist.
0.040
ASP1 N SOL171 OW 0.020
ASP1 N SOL172 OW 0.020
ASP1 N SOL175 OW 0.100
ASP1 N SOL177 OW 0.020
ASP1 N SOL179 OW 0.020
.
.
.
.
SOL682OW HIS13 O 0.020
SOL682OW GLN15 OE1 0.020
SOL682OW GLN15 NE2 0.040
SOL682OW ALA21 O 0.020
SOL682OW GLU22 OE1 0.140
Delete the original file and run the script again. The output is simply
appended if the same file is already present. Or, modify the output routines.
The latter part of the file is the expected output.
-Justin
Kind regards,
chetan.
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: 13 December 2010 19:54
To: Gromacs Users' List
Subject: Re: [gmx-users] HBOND probability
Poojari, Chetan wrote:
Hello Justin,
I commented out the lines from 151-161
# unless ($resn =~ /SOL/) {
# for (my $z=1; $z=$nres; $z++) {
#if ($donors{$z} == $natom) {
#$donor_names[$z] = $name;
#$donor_resn[$z] = join('', $resn, $resnum);
# } elsif ($acceptors{$z} == $natom) {
# $acceptor_names[$z] = $name;
# $acceptor_resn[$z] = join('', $resn, $resnum);
# }
# }
# }
I am ending up with the similar output.
Please comment out *just* the unless line
[gmx-users] Umberella sampling
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html -- original message -- I can't understand correctly what we do when we are using umberella sampling for obtaining PMF. I explain that ,please modify or complete it. (I think we define some sampling windows,each related to an reference distance. for each distance ,relative to it's distance,we define a spring constant. our spring is at rest in the center of windows, then we do a short simulation within each windows such that our molecule is connected to the spring and it's potential energy is depending to it's displacement from the center of windows. Then we have potential energy of two molecules in any distance from each other. Having potential energy along the reaction path or here falong the degree of freedom(distance between two molecules) is PMF oof interest and the difference between limits of PMF plot is delta-free energy of interest) what do you think ?do you agree with me? Thanks in advance for your atteintion. Mohsen -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: gb_saltconc in implicit water simulations
Can anyone answer this question or guide me somewhere with helpful information? Thanks, Bob On Thu, Dec 9, 2010 at 4:52 PM, Bob Johnson bobjohnson1...@gmail.comwrote: Hello everyone, I am trying to use implicit solvent with a CG DNA model. The model, however, uses explicit charges, which means that the DNA carries an overall negative charge. When using implicit solvent with a charged system in other codes (e.g. Amber), the electrolyte is taken care of implicitly as well. However, in Gromacs this is currently not implemented since gb_saltconc is always set to 0. Without any salt, the DNA duplex is obviously unstable. Are there plans on implementing implicit counterions so that one can set gb_saltconc to nonzero values? It doesn't seem natural to include explicit counterions to neutralize the system when using implicit solvent. Is there a typical protocol one follows to neutralize charged systems when using implicit solvent? Thanks, Bob -- Bob Johnson, PhD Institute for Computational Molecular Science Temple University 1900 North 12th Street Philadelphia, PA 19122 http://astro.temple.edu/~rjohnson http://astro.temple.edu/%7Erjohnson -- Bob Johnson, PhD Institute for Computational Molecular Science Temple University 1900 North 12th Street Philadelphia, PA 19122 http://astro.temple.edu/~rjohnson -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: gb_saltconc in implicit water simulations
On 14/12/10 18:35, Bob Johnson wrote: Can anyone answer this question or guide me somewhere with helpful information? Thanks, Bob I was going to send a very similar mail -namely, I have a coarse-grain system in vacuum where I'd like to simulate a charged polymer. My idea was that of adding a single ghost counter-ion with zero VdW interactions, perhaps keeping it fixed in one corner of the box, but I'd like to know how meaningful it is. thanks! m. On Thu, Dec 9, 2010 at 4:52 PM, Bob Johnson bobjohnson1...@gmail.com mailto:bobjohnson1...@gmail.com wrote: Hello everyone, I am trying to use implicit solvent with a CG DNA model. The model, however, uses explicit charges, which means that the DNA carries an overall negative charge. When using implicit solvent with a charged system in other codes (e.g. Amber), the electrolyte is taken care of implicitly as well. However, in Gromacs this is currently not implemented since gb_saltconc is always set to 0. Without any salt, the DNA duplex is obviously unstable. Are there plans on implementing implicit counterions so that one can set gb_saltconc to nonzero values? It doesn't seem natural to include explicit counterions to neutralize the system when using implicit solvent. Is there a typical protocol one follows to neutralize charged systems when using implicit solvent? Thanks, Bob -- Bob Johnson, PhD Institute for Computational Molecular Science Temple University 1900 North 12th Street Philadelphia, PA 19122 http://astro.temple.edu/~rjohnson http://astro.temple.edu/%7Erjohnson -- Bob Johnson, PhD Institute for Computational Molecular Science Temple University 1900 North 12th Street Philadelphia, PA 19122 http://astro.temple.edu/~rjohnson -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: gb_saltconc in implicit water simulations
devicerandom wrote: On 14/12/10 18:35, Bob Johnson wrote: Can anyone answer this question or guide me somewhere with helpful information? Thanks, Bob I was going to send a very similar mail -namely, I have a coarse-grain system in vacuum where I'd like to simulate a charged polymer. My idea was that of adding a single ghost counter-ion with zero VdW interactions, perhaps keeping it fixed in one corner of the box, but I'd like to know how meaningful it is. In vacuum and implicit solvent are very different concepts. If you are indeed simulating in a vacuum, I would be willing to bet that your charged polymer will rapidly associate with your dummy ion simply due to attractive Coulombic interactions that are not screened by any intervening solvent. In regards to the original post, I have seen this question asked and ignored several times already, unfortunately. Most of the literature I have read (which primarily uses CHARMM) does not specify how counterions are handled, if at all. Maybe there is some intrinsic compensating factor in CHARMM that I simply don't know about. I found this: http://dx.doi.org/10.1002/jcc.20874 But again, it uses CHARMM and fancy modified electrostatic models. I would really hope that someone who knows about the proper GROMACS methodology would comment. This has been a curiosity of mine for some time, as well. I have not had a pressing need to try out the implicit solvent features, but in the absence of being sure of the methodology, I am unlikely to do so. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: gb_saltconc in implicit water simulations
On 14/12/10 19:04, Justin A. Lemkul wrote: I was going to send a very similar mail -namely, I have a coarse-grain system in vacuum where I'd like to simulate a charged polymer. My idea was that of adding a single ghost counter-ion with zero VdW interactions, perhaps keeping it fixed in one corner of the box, but I'd like to know how meaningful it is. In vacuum and implicit solvent are very different concepts. If you are indeed simulating in a vacuum, I would be willing to bet that your charged polymer will rapidly associate with your dummy ion simply due to attractive Coulombic interactions that are not screened by any intervening solvent. Heh, I know very well that -and that is one of the reasons I wanted to know how does one cope with that. I mean, if it's a single polymer, perhaps one can naively position restrain the ion in a corner of the box, away from the polymer, while the polymer stays on its center of mass. But if I want multiple objects in my box, I guess it's not going to work. I'd like very much to use implicit solvent as well but I have to see how deep is the performance impact on my model -after all, one does coarse grain to be raw but *fast* :) In regards to the original post, I have seen this question asked and ignored several times already, unfortunately. Most of the literature I have read (which primarily uses CHARMM) does not specify how counterions are handled, if at all. Maybe there is some intrinsic compensating factor in CHARMM that I simply don't know about. I found this: http://dx.doi.org/10.1002/jcc.20874 But again, it uses CHARMM and fancy modified electrostatic models. I would really hope that someone who knows about the proper GROMACS methodology would comment. This has been a curiosity of mine for some time, as well. I have not had a pressing need to try out the implicit solvent features, but in the absence of being sure of the methodology, I am unlikely to do so. Perhaps the developers of the implicit solvent know about that? I hope so... m. -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: gb_saltconc in implicit water simulations
Hi! Sorry that I missed this discussion, we recently moved the lab and there where quite many things to attend to. When we did the implementation of implicit solvent into Gromacs, one of the strong points was to see how fast we could make it, to speed up conformational sampling as much as possible. Adding in the extra Debye-Huckel term for a non-zero salt-concentration was not a priority at the time. It might be a bit unfortunate that the option anyway exists in the mdp-file. I will try and see if I can find the time to put it in, but that will not happen in the next coming weeks although I agree that it would be very useful to have :-) When it comes to the use of explicit ions in an implicit solvent, I hate to say that I'm not much of an expert, really. Having said that, and someone else is very welcome to correct me on this point, there does not seem to exist a wide body of literature about this. In addition to the paper that Justin pointed to, there is some work done by Michael Feig (eg. http://www.ncbi.nlm.nih.gov/pubmed/16928023). Also I think that particularly with DNA there are problems with the theory itself as it does not handle high salt-concentrations very well. Cheers /Per 14 dec 2010 kl. 20.22 skrev devicerandom: On 14/12/10 19:04, Justin A. Lemkul wrote: I was going to send a very similar mail -namely, I have a coarse-grain system in vacuum where I'd like to simulate a charged polymer. My idea was that of adding a single ghost counter-ion with zero VdW interactions, perhaps keeping it fixed in one corner of the box, but I'd like to know how meaningful it is. In vacuum and implicit solvent are very different concepts. If you are indeed simulating in a vacuum, I would be willing to bet that your charged polymer will rapidly associate with your dummy ion simply due to attractive Coulombic interactions that are not screened by any intervening solvent. Heh, I know very well that -and that is one of the reasons I wanted to know how does one cope with that. I mean, if it's a single polymer, perhaps one can naively position restrain the ion in a corner of the box, away from the polymer, while the polymer stays on its center of mass. But if I want multiple objects in my box, I guess it's not going to work. I'd like very much to use implicit solvent as well but I have to see how deep is the performance impact on my model -after all, one does coarse grain to be raw but *fast* :) In regards to the original post, I have seen this question asked and ignored several times already, unfortunately. Most of the literature I have read (which primarily uses CHARMM) does not specify how counterions are handled, if at all. Maybe there is some intrinsic compensating factor in CHARMM that I simply don't know about. I found this: http://dx.doi.org/10.1002/jcc.20874 But again, it uses CHARMM and fancy modified electrostatic models. I would really hope that someone who knows about the proper GROMACS methodology would comment. This has been a curiosity of mine for some time, as well. I have not had a pressing need to try out the implicit solvent features, but in the absence of being sure of the methodology, I am unlikely to do so. Perhaps the developers of the implicit solvent know about that? I hope so... m. -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] gmx-4.5.3 CMake build fails
On 14/12/2010 8:02 PM, Reinhold Bader wrote: Hello, building gromacs 4.5.3 with Cmake 2.6.3 fails because the build system cannot link g_analyze Linking C executable g_analyze ../gmxlib/libgmx.a(gmx_matrix.c.o): In function `matrix_invert': gmx_matrix.c:(.text+0x1d62): undefined reference to `dgetrf_' gmx_matrix.c:(.text+0x2442): undefined reference to `dgetri_' Note that I have GMX_EXTERNAL_BLAS -- ON GMX_EXTERNAL_LAPACK -- ON and the subsequently requested MKL_ settings have been properly inserted. I've tried to work around this by also adding the MKL libraries to CMAKE_EXE_LINKER_FLAGS, without avail. Use make VERBOSE=1 and see how the produced linker line agrees with your MKL documentation. Mark -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] md.log
Hi Itamar, Thanks for your help. Without the md.log file i could able to extend the simulation time but i could not able to append to results to my old .trr and .edr files. Rama On Mon, Dec 13, 2010 at 6:39 PM, Itamar Kass itamar.k...@monash.edu wrote: Hi, the log file is not needed for extension. Use something like: grompp -f md_extension.mdp -c MD_01.gro -n system.ndx -p system.top -t MD_01.trr -r MD_01.edr -o MD_02.tpr Itamar On 14/12/10 1:29 PM, Ramachandran G wrote: Hi gmx-users: I am trying to extend my simulation run but unfortunately i deleted the file md.log. Is there any way i get my md.log file using the existing .edr or .trr files so that i can proceed further. Thank you. Rama -- In theory, there is no difference between theory and practice. But, in practice, there is. - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@monash.edu -- gmx-users mailing list gmx-us...@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Postdoctoral Research Scholar, Department of Chemistry, University of Nevada, Reno. -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] md.log
On 15/12/2010 10:07 AM, Ramachandran G wrote: Hi Itamar, Thanks for your help. Without the md.log file i could able to extend the simulation time but i could not able to append to results to my old .trr and .edr files. That is what trjcat and eneconv are for. Mark Rama On Mon, Dec 13, 2010 at 6:39 PM, Itamar Kassitamar.k...@monash.edu wrote: Hi, the log file is not needed for extension. Use something like: grompp -f md_extension.mdp -c MD_01.gro -n system.ndx -p system.top -t MD_01.trr -r MD_01.edr -o MD_02.tpr Itamar On 14/12/10 1:29 PM, Ramachandran G wrote: Hi gmx-users: I am trying to extend my simulation run but unfortunately i deleted the file md.log. Is there any way i get my md.log file using the existing .edr or .trr files so that i can proceed further. Thank you. Rama -- In theory, there is no difference between theory and practice. But, in practice, there is. - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@monash.edu -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] freezegrps concept
Hello I am trying to simulate lipase in water in ffamber99sb-ildn. Chosen cubic as box with distance of 1nm b/w solute n box. Protein is going out of the box after equilibration step. Any solution? Should i use *freezegrps* option to restrict protein movement. Please provide some light to this option. What effect it will have on the whole system? -- Yuvraj -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] freezegrps concept
YUVRAJ UBOVEJA wrote: Hello I am trying to simulate lipase in water in ffamber99sb-ildn. Chosen cubic as box with distance of 1nm b/w solute n box. Protein is going out of the box after equilibration step. Any solution? FAQ #11. http://www.gromacs.org/Documentation/FAQs Please also note that if you search for a generic phrase like protein out of box on the mailing list archive, your answer will turn up as the first post (and then several hundred more). Should i use *freezegrps* option to restrict protein movement. Please provide some light to this option. What effect it will have on the whole system? If you're trying to fit the position of the protein into some preconceived notion of what it should be doing, stop. If you are trying to appropriately equilibrate the solvent while keeping the protein fixed (in any arbitrary location), position restraints are much easier because: 1. They are already present in the topology and are easily invoked 2. Freezing is incompatible with pressure coupling 3. If proper energygrp_excl are not used, you can end up generating very large forces -Justin -- Yuvraj -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] freezegrps concept
On Wed, Dec 15, 2010 at 12:53 AM, YUVRAJ UBOVEJA yuvrajthe...@gmail.comwrote: Hello I am trying to simulate lipase in water in ffamber99sb-ildn. Chosen cubic as box with distance of 1nm b/w solute n box. Protein is going out of the box after equilibration step. Any solution? The protein does not diffuse out of the box. Use for eg: trjconv -pbc nojump on your trajectory. For more information refer to the link below... http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions Best Wishes, Sarath Should i use *freezegrps* option to restrict protein movement. Please provide some light to this option. What effect it will have on the whole system? -- Yuvraj -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] HPC mpi how to run
Hi , I have installed PSFTP and PuTTY. I have seen the Gromacs-4.0.7 in ./opt in wivenhoe (cluster), and i know how to upload my file to my folder using PSFTP. However i donot know how to run it in HPC; when i using Gromacs-4.0.7 in my desktop, if the Gromacs is installed properly, there will be a line when i type the command 'luck'. How can i see the gromacs whether it istalled properly? how can i run simulations on HPC? Thanks! -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] HPC mpi how to run
gromacs wrote: Hi , I have installed PSFTP and PuTTY. I have seen the Gromacs-4.0.7 in ./opt in wivenhoe (cluster), and i know how to upload my file to my folder using PSFTP. However i donot know how to run it in HPC; when i using Gromacs-4.0.7 in my desktop, if the Gromacs is installed properly, there will be a line when i type the command 'luck'. How can i see the gromacs whether it istalled properly? how can i run simulations on HPC? Add the Gromacs installation to your PATH and proceed as you would anything else. Beyond that, consult your sysadmin for help. The exact sequence of commands will be dictated by your MPI environment, presence/absence of a queuing system, etc. -Justin Thanks! -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Appropriate (desktop) hardware for Gromacs
On 15/12/2010 1:03 PM, Tom Dupree wrote: Greetings all, We are looking at setting up Linux desktop in our lab for setting up some simulations to be run externally, as well some short simulations. I am new to Linux and Gromos. I'm going to presume you mean GROMACS. I have done some reading of the gmx-users list archive and have a few questions. I was wondering if there is anything in particular to avoid/choose in terms of hardware for such a system? Since you are not running with MPI parallelism, no. Specifically does Gromos prefer a particular architecture? (INTEL/AMD) No. Any chip with SSE or SSE2 is fine. I understand there is now some GPU computing support with Gromos, are there any problems using consumer grade cards? (GeForce GTX 460/480) The manual lists some compatible cards. Is Gromos happier in a particular flavour of Linux, given we will be running on a desktop? No. Some distros do have GROMACS available via their package managers (usually in their extras section). Mark Thanks for your time in looking at these (noobish) questions. Tom -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Re: [gmx-users] ERROR: Source code file: statutil.c, line: 727
Uday, You are reproducing the output of md.csh. I would also like to see the contents of md.csh to know the gromacs commands therein. This would help to see where the error is coming. Please paste the file md.csh. sharada -- Original Message -- From: udaya kiran kiran.ud...@gmail.com To: Sarath Chandra sarathchandrada...@gmail.com Cc: Discussion list for GROMACS users gmx-users@gromacs.org Date: Tue, 14 Dec 2010 11:13:05 +0100 Subject: Re: [gmx-users] ERROR: Source code file: statutil.c, line: 727 Hello, Here I am sending the complete output after the md.csh command with the errors in bold. COMMAND: csh md.csh :-) G R O M A C S (-: Groningen Machine for Chemical Simulation :-) VERSION 4.0.5 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.orghttp://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp (double precision) (-: Option Filename Type Description -f md-md.mdp Input, Opt! grompp input file with MD parameters -po inmd.mdp Output grompp input file with MD parameters -c results/eq1bar300K.gro Input Structure file: gro g96 pdb tpr tpb tpa -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -n Index_sol.ndx Input, Opt! Index file -p topol_sol_hbond_131210.top Input Topology file -pp processed.top Output, Opt. Topology file -o inmd.tpr Output Run input file: tpr tpb tpa -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt -e ener.edr Input, Opt. Energy file: edr ene Option Type Value Description -- -[no]h bool no Print help info and quit -nice int 0 Set the nicelevel -[no]v bool yes Be loud and noisy -time real -1 Take frame at or first after this time. -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -maxwarn int 0 Number of allowed warnings during input processing -[no]zero bool no Set parameters for bonded interactions without defaults to zero instead of generating an error -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes ERROR --- Program grompp, VERSION 4.0.5 Source code file: statutil.c, line:
