Re: FudgeLJ in ffamber - Was: [gmx-users] Re: fudgeQQ (again ...)
Hi,
On Feb 13, 2007, at 6:52 AM, Jones de Andrade wrote:
Hi guys.
Well, I'm not "exactly" trying t reopen an old discussion. I'm
trying to see a different aspect from it, as the subject indicates.
Since the message reproduced below is the last of the "fudges"
questions, I'm worried about the fact of the fudgeLJ meaning
nothing for the simulation.
First, is it true, and there is no way around to get a working
fudge LJ of 0.5 AND a fudgeQQ of 0.8333 in gromacs simulations?
No, you can certainly use fudge factors with Gromacs.
Essentially:
1. If you do not generate 1,4 ("pair") interactions they will be zero
unless you specify them explicitly.
2. If you do generate them, standard combination rules of the force
field will be applied, combined with the fudge factor.
3. If you generate pairs and still specify some interactions, those
will override the generated values.
Cheers,
Erik
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FudgeLJ in ffamber - Was: [gmx-users] Re: fudgeQQ (again ...)
Hi guys. Well, I'm not "exactly" trying t reopen an old discussion. I'm trying to see a different aspect from it, as the subject indicates. Since the message reproduced below is the last of the "fudges" questions, I'm worried about the fact of the fudgeLJ meaning nothing for the simulation. First, is it true, and there is no way around to get a working fudge LJ of 0.5 AND a fudgeQQ of 0.8333 in gromacs simulations? Having this in mind, shouldn't it mean that the ffamber, the amber port to gromacs, have a "problem" in that point? Specially because it uses, up to the point I could see, the same "configurations" in the "default" section? I have deep concerns on this because I would like to move on to gromacs to make the next simulations I'm interested in. My interests in gromacs range from its speed to simplicity and range of analysis programs it already have (and, of course, the cost of the program). But this specific point is a big reason of concern to me, and I would like to see it clarified. Thanks a lot for any help in advance. Sincerally yours, Jones On 12/7/06, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote: > I am puzzled about this. In your opinion, when I use genpairs=no, fudgeLJ= > 0.5 and fudgeQQ=0.8333, are these scaling factors, 0.5 and 0.8333, useful? > On the other hand, when using genpairs=yes, how to set the scaling factor of > fudgeLJ and fudgeQQ?$ fudgeQQ is always used no matter what the value of genparis is. (exerpt from http://www.gromacs.org/pipermail/gmx-users/2006-September/023743.html) Each force-field has its own rules (e.g. gen-pairs and FudgeLJ/QQ), but these apply to the information outlined above. For example, gen-pairs does NOT mean "generate a [ pairs ] section for the molecule." Instead, it means "If LJ-14 epsilon and sigma are not present in a [ pairs ] section entry, and that type of interaction is not explicitly formulated in [ pairtypes ], then it is permissible to use the regular non-bonded parameters, and in that case scale them by FudgeLJ." Therefore your settings indicate that coulombic 1-4 interactions will be scaled by 0.8333 and the pairs must be taken directly from the [ pairs ] or [ pairtypes ] section (and they will NOT be scaled by fudgeLJ). In your case fudgeLJ does not matter (you could change the value and it would not affect your simulation). However, I have always hoped that it is set to 0.5 to indicate that this is what the forcefield developers have done for you and included it in [ pairtypes ] so that it's kind of a reference value for your piece of mind. I was assuming that the previous messages were from an Amber forcefield. Since Amber uses (to my knowledge) [ pairtypes ] instead of genpairs=yes, I was confused by the combination of genpairs=yes and fudgeQQ=0.8333. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] 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 don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] problem still lies regarding dssp
"Naser, Md Abu " <[EMAIL PROTECTED]> wrote: Yes Abu, I have seen it, while executing do_dssp with the .xtc file I have seen those commands. regards SANGEETA Hi Sangeeta, Your out dose not say that the programme is really running. Can you try with .trr and .tpr file and see you get something at the bottom of the output like: Reading frame 0 time0.000 Back Off! I just backed up ddQmCBhK to ./#ddQmCBhK.1# Reading frame 20 time 40.000 Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of sangeeta kundu Sent: Mon 12/02/2007 9:55 AM To: Discussion list for GROMACS users Subject: RE: [gmx-users] problem still lies regarding dssp Dear Abu and Mark, You asked me, whether my computer is shared by many, it is not, I think the program was not hanged because while executing do_dssp -v as usual Gromacs output was given, ":-) G R O M A C S (-: GROningen Mixture of Alchemy and Childrens' Stories :-) VERSION 3.3.1 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2006, 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. :-) do_dssp (-: Option Filename Type Description -f traj.xtc InputGeneric trajectory: xtc trr trj gro g96 pdb -s topol.tpr InputStructure+mass(db): tpr tpb tpa gro g96 pdb xml -n index.ndx Input, Opt. Index file -ssdump ssdump.dat Output, Opt. Generic data file -map ss.map Input, Lib. File that maps matrix data to colors -o ss.xpm Output X PixMap compatible matrix file -sc scount.xvg Output xvgr/xmgr file -a area.xpm Output, Opt. X PixMap compatible matrix file -tatotarea.xvg Output, Opt. xvgr/xmgr file -aa averarea.xvg Output, Opt. xvgr/xmgr file Option Type Value Description -- -[no]h bool no Print help info and quit -[no]X bool no Use dialog box GUI to edit command line options -niceint 19 Set the nicelevel -b time 0 First frame (ps) to read from trajectory -e time 0 Last frame (ps) to read from trajectory -dt time 0 Only use frame when t MOD dt = first time (ps) -tu enum ps Time unit: ps, fs, ns, us, ms or s -[no]w bool no View output xvg, xpm, eps and pdb files -[no]xvgr boolyes Add specific codes (legends etc.) in the output xvg files for the xmgrace program -sss string HEBT Secondary structures for structure count " I changed the permission of dsspcmbi and dsspcmbi.exe files , what else I should do? I mean execpt these two files what are the other files that need change of permission now these two files has read, write, and executable permission, Mark suggested me to call dssp "by hand", will you please explain in more detail?? In order to get taht particular coloured map what procedure should I adopt?? regards SANGEETA "Naser, Md Abu " <[EMAIL PROTECTED]> wrote: Hi Sangeeta, Let me ask you few questions in order to solve the problem. Are you sure your do_dssp prog were running or it was hanged? To make sure please try using verbose output using -v option. Is your computer shared among too many people? What is the file permission status of dssp? To find out use: ls -l /directory/where/you/put/dssp If you see any restricton to file permission change it to chmod a+rx dssp Hope this will help. Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of sangeeta kundu Sent: Fri 09/02/2007 10:13 AM To: gmx-users@gromacs.org Subject: [gmx-users] problem still lies regarding dssp Dear All, I do not know whether I am interrupting you again and again by asking the same question, but I am helpless , I can not detect my fault, When I run the program DSSP it works fine, but while executing do_dssp or my_dssp (as suggested by Yang) the program seems to be never ending, intermedi
Re: [gmx-users] loss of information trr xtc
Qiao Baofu wrote: If I understand correctly, only the coordinate information can be saved in .xtc. That means, all other informations, velocity, force, etc, can't be reconverted into .trr again. Yes. Loosely speaking, the xtc format stores only the changes in position, which requires only low precision since the positions don't change much from step to step and so conserving space. Since the velocities and forces can change radically, there's no advantage to be gained here. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] restarting a sorted shuffled trajectory
Your specific problem is probably because you sent unsorted
(=desorted) .trr file to grompp -sort. Due to the order that grompp
does things, the .trr must already be appropriately sorted at the time
that it is read in. This is the reason for the complicated procedure
that I outlined in the description section of g_desort.
Also, and I can't stress this enough: If you want to use grompp -sort
to start and then continue by anything other than tpbconv, you need to
use g_desort and NOT trjconv -n deshuffle.ndx. For the procedure that
I outline you may as well delete deshuffle.ndx as soon as it is created.
I sent more complete information previously but it bounced back. Here
it is again. Hopefully it is not a double post.
#
The instructions are in g_desort.
http://www.gromacs.org/pipermail/gmx-users/2007-January/025584.html
I think you misunderstand one key thing: use g_desort to go from a
totally mangled
trajectory to a totally unmangled trajectory. If you use g_desort then
you shouldn't need
the deshuffle.ndx file that was output from trjconv and definately do
not first deshuffle
and then use g_desort. The program really should be called
g_deshuffledesort but that
seemed like a too long name.
I have by now fully tested this and I use it for all of my large runs.
The key test that
convinced me is that after I put tens of 200ps pieces back together
(trjcat the
desorteddeshuffled .xtc files) I use g_msd to calculate the MSD vs.
time for water and I
get a straight line without any inconsistencies at the shuffle/sort
junctures. Also I
have used VMD to view independent water molecules and things are all
looking good.
The benefit of sort tends to deteriorate over time so I find it best
to do cycles of
about 200ps. This said, shuffling and sorting my runs gives me 100%
efficiency to 4cpus =
they run 4x as fast as they do on a single node. I can't come anywhere
near that with
plain runs.
Here is a sample script that I use to run a cycle. After running this
once through I
simply increment the $in and $out values and run again. Actually I
have template
submission scripts and then a daemon that uses sed to put the correct
numbers in the
correct places to make a new input script for submission each round.
I took a look at your specific information and there is not enough
there. Please specify
how you are doing your desorting. Also, please take a look at the
source code where it
contains a description of how to use the program. Note that you need
to deshuffle/desort
to get something that you can look at but then you need to re-sort
your trr according to
the new sorting scheem that will be different than the last one and is
currently unknown.
To do this you do a trial grompp that allows you to generate a ndx
that can take your
normal .trr to a properly sorted/shuffled trr for input.
Sorry that it's so confusing but it's the only way that I could think
of. So here is the
sample script first and then after that I have attached the notes that
are included in
g_desort.c.
I am happy that this has found someone else that is interested in
using it. Please feel
free to direct and more questions to this list.
#!/bin/sh
#$ -v
LD_LIBRARY_PATH=/usr/lib64/tls:/hpf/tools/n1ge/lib/lx24-amd64:/tools/lam/lam-7.1.2/lib
#$ -v
PATH=/hpf/tools/n1ge/bin/lx24-amd64:/usr/local/bin:/usr/bin:/usr/X11R6/bin:/bin:/usr/games:/opt/gnome/bin:/tools/local/bin:/home/cneale/exe:/projects/pomes/cneale/exe/gromacs-3.3.1/exec/fftw-3.1.2/bin:.:/tools/lam/lam-7.1.2/bin
MYMOL=sys1800
ED=/projects/pomes/cneale/exe/gromacs-3.3.1/exec/fftw-3.1.2/bin
DD=/projects/pomes/cneale/exe/gromacs-3.3.1/exec/fftw-3.1.2/share/gromacs/template
MD=/projects/pomes/cneale/micelle/2huge
cd ${MD}
in="_md25"
out="_md26"
mynp=8
echo "Starting grompp..."
#Shuffle the .trr input file correctly. Assume that it is not
currently shuffled
${ED}/grompp -np ${mynp} -shuffle -sort -f ${MYMOL}${out}.mdp -c
${MYMOL}${in}_deshuffleddesorted.gro -p ${MYMOL}.top -n ${MYMOL}.ndx -o
${MYMOL}${out}_a.tpr -deshuf deshuffle${out}_a.ndx>
output.${MYMOL}_grompp${out}_a 2>
output.${MYMOL}_grompp${out}_e_a
rm -f deshuffle${out}_a.ndx mdout.mdp
echo System | ${ED}/editconf -f ${MYMOL}${out}_a.tpr -o
${MYMOL}${out}_shuffledsortedInit_a.gro
#g_desort -f original shuffled will unshuffle
#Assuming that g_desort -f shuffled original will REshuffle
${DD}/g_desort -f ${MYMOL}${out}_shuffledsortedInit_a.gro
${MYMOL}${in}_deshuffleddesorted.gro -o reshuffleresort${MYMOL}${out}_a.ndx
${ED}/trjconv -f ${MYMOL}${in}_deshuffleddesorted.trr -o
${MYMOL}${in}_reshuffleresort.trr -n ./reshuffleresort${MYMOL}${out}_a.ndx
#Create the run input file
${ED}/grompp -np ${mynp} -shuffle -sort -f ${MYMOL}${out}.mdp -c
${MYMOL}${in}_deshuffleddesorted.gro -t
${MYMOL}${in}_reshuffleresort.trr -p ${MYMOL}.top
-n ${MYMOL}.ndx -deshuf deshuffle${out}.ndx -e ${MYMOL}${in}.edr -o
${MYMOL}${out}.tpr >
output.${M
Re: [gmx-users] restarting a sorted shuffled trajectory
No. You don't need to "desort" it. But from your error message, it seems not related to "shuffling and sorting" but between your .top and .gro. Did you "deshuffle" toto_min_formd.gro? Can you check your .top and .gro more carefully? Regards, Yang Ye On 2/13/2007 2:05 AM, Alan Dodd wrote: >From memory, deshuffling, followed by using editconf to change confout.gro to a pdb and back again, results in the molecule types all being in the same order again (in my case, protein, lipid, solvent, ions instead of protein, lipid, ions, water, lipid, ions, water, lipid, ions, water, protein etc). Actually... I think ions might move about, but this process at leasts put them all in the same place, even if you then have to check which order the groups are in. I couldn't say for certain if the molecules within a set group stay in the same order, but this can at least let you use the same .top with minimal or no alterations. - Original Message From: Stéphane Téletchéa <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Monday, February 12, 2007 5:00:24 PM Subject: [gmx-users] restarting a sorted shuffled trajectory Dear all, I'm willing to do a fine-tuning start for my simulation using multiples prX.mdp input. I'm launching the first run using -shuffle -sort from grompp (with pr1.mdp), but i'd like to know how to reuse the resulting .trr file for the second pr (pr2.mdp). I've tried deshuffling first the trr file but do i also need to desort it ? (as Chris Neale posted on 24.01.2007 on this list) So far, i'm getting: Warning: atom names in ../test_min_deflated26_sol_ions.top and ../toto_min_formd.gro don't match (HW2 - HW1) (more than 20 non-matching atom names) WARNING 1 [file "../test_min_deflated26_sol_ions.top", line 38]: 23642 non-matching atom names atom names from ../test_min_deflated26_sol_ions.top will be used atom names from ../OR1G1_min_formd.gro will be ignored The mdrun was launched after this grompp input : grompp_lam \ -f mdp/md_Na.mdp \ -p test_min_deflated26_sol_ions.top \ -pp test_min_deflated26_sol_ions_out.top \ -c toto_min_formd.gro \ -o fullmd_ions.tpr \ -po md_Na_out.mdp \ -deshuf fullmd_ions.ndx \ -shuffle \ -sort \ -np 4 I'd like to pursue the dynamics, so far i'm doing: cd test grompp_lam \ -f ../mdp/pr1.mdp \ -p ../test_min_deflated26_sol_ions.top \ -pp test_out.top \ -c ../toto_min_formd.gro \ -t ../fullmd_ions_deshuf.trr \ -e ../fullmd_ions.edr \ -n toto_min_formd.ndx \ -o test.tpr \ -po test_out.mdp \ -np 4 Thanks a lot for your comments/advices. Cheers, Stéphane ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] restarting a sorted shuffled trajectory
>From memory, deshuffling, followed by using editconf to change confout.gro to >a pdb and back again, results in the molecule types all being in the same >order again (in my case, protein, lipid, solvent, ions instead of protein, >lipid, ions, water, lipid, ions, water, lipid, ions, water, protein etc). >Actually... I think ions might move about, but this process at leasts put them >all in the same place, even if you then have to check which order the groups >are in. I couldn't say for certain if the molecules within a set group stay >in the same order, but this can at least let you use the same .top with >minimal or no alterations. - Original Message From: Stéphane Téletchéa <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Monday, February 12, 2007 5:00:24 PM Subject: [gmx-users] restarting a sorted shuffled trajectory Dear all, I'm willing to do a fine-tuning start for my simulation using multiples prX.mdp input. I'm launching the first run using -shuffle -sort from grompp (with pr1.mdp), but i'd like to know how to reuse the resulting .trr file for the second pr (pr2.mdp). I've tried deshuffling first the trr file but do i also need to desort it ? (as Chris Neale posted on 24.01.2007 on this list) So far, i'm getting: Warning: atom names in ../test_min_deflated26_sol_ions.top and ../toto_min_formd.gro don't match (HW2 - HW1) (more than 20 non-matching atom names) WARNING 1 [file "../test_min_deflated26_sol_ions.top", line 38]: 23642 non-matching atom names atom names from ../test_min_deflated26_sol_ions.top will be used atom names from ../OR1G1_min_formd.gro will be ignored The mdrun was launched after this grompp input : grompp_lam \ -f mdp/md_Na.mdp \ -p test_min_deflated26_sol_ions.top \ -pp test_min_deflated26_sol_ions_out.top \ -c toto_min_formd.gro \ -o fullmd_ions.tpr \ -po md_Na_out.mdp \ -deshuf fullmd_ions.ndx \ -shuffle \ -sort \ -np 4 I'd like to pursue the dynamics, so far i'm doing: cd test grompp_lam \ -f ../mdp/pr1.mdp \ -p ../test_min_deflated26_sol_ions.top \ -pp test_out.top \ -c ../toto_min_formd.gro \ -t ../fullmd_ions_deshuf.trr \ -e ../fullmd_ions.edr \ -n toto_min_formd.ndx \ -o test.tpr \ -po test_out.mdp \ -np 4 Thanks a lot for your comments/advices. Cheers, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 134 652 891 78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Bored stiff? Loosen up... Download and play hundreds of games for free on Yahoo! Games. http://games.yahoo.com/games/front ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Nucleic Acids -- Protonate ?
Thanks Mark, David, Yang, Joern and Maik for your suggestions. Now the only way I see is to use amber forcefield for nucleic acid simulations. Regards, Vissu. P.S. : **keywords : Nucleic Acids, DNA, RNA, Gromacs, AMBER FF, MD simulations On 2/12/07, Maik Goette <[EMAIL PROTECTED]> wrote: > I don't know how to solve your problem, but merely adding counter-ions > because you don't know where or how many hydrogens there might be is > almost guaranteed to lead to a simulation that has no correlation with > reality. The answer to the problem has been presented (amber FF port), but I thought exactly the same...and btw...Mark, the one with the car mechanic was great...;) Best regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Mark Abraham wrote: > Viswanadham Sridhara wrote: >> Hello, >> >> I wanted to perform MD simulation on a DNA structure I found from >> RCSB.org. After changing C, G, A, T to DCYT, DGUA, DADE and DTHY >> respectively, I used pdb2gmx to create topology file. It says missing >> hydrogens, which is obvious and I realized I could not use protonate >> command as ffgmx2.hdb does not have these residues to be protonated. >> Is there any other file to add missing hydrogens or Is there any other >> program which you can use to add missing hydrogens to nucleic acids. >> The total charge now is -43e, which is quite huge, and I am looking to >> see electric field effects on the DNA. This will be a lot of charge to >> neutralize by adding counter-ions, if I ignore hydrogens. > > I don't know how to solve your problem, but merely adding counter-ions > because you don't know where or how many hydrogens there might be is > almost guaranteed to lead to a simulation that has no correlation with > reality. > > Mark > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to [EMAIL PROTECTED] > 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 don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Viswanadham Sridhara, Research Assistant, Old Dominion University, Norfolk, Va-23529. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Nucleic Acids -- Protonate ?
> I don't know how to solve your problem, but merely adding counter-ions > because you don't know where or how many hydrogens there might be is > almost guaranteed to lead to a simulation that has no correlation with > reality. The answer to the problem has been presented (amber FF port), but I thought exactly the same...and btw...Mark, the one with the car mechanic was great...;) Best regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Mark Abraham wrote: Viswanadham Sridhara wrote: Hello, I wanted to perform MD simulation on a DNA structure I found from RCSB.org. After changing C, G, A, T to DCYT, DGUA, DADE and DTHY respectively, I used pdb2gmx to create topology file. It says missing hydrogens, which is obvious and I realized I could not use protonate command as ffgmx2.hdb does not have these residues to be protonated. Is there any other file to add missing hydrogens or Is there any other program which you can use to add missing hydrogens to nucleic acids. The total charge now is -43e, which is quite huge, and I am looking to see electric field effects on the DNA. This will be a lot of charge to neutralize by adding counter-ions, if I ignore hydrogens. I don't know how to solve your problem, but merely adding counter-ions because you don't know where or how many hydrogens there might be is almost guaranteed to lead to a simulation that has no correlation with reality. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] 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 don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] restarting a sorted shuffled trajectory
Dear all, I'm willing to do a fine-tuning start for my simulation using multiples prX.mdp input. I'm launching the first run using -shuffle -sort from grompp (with pr1.mdp), but i'd like to know how to reuse the resulting .trr file for the second pr (pr2.mdp). I've tried deshuffling first the trr file but do i also need to desort it ? (as Chris Neale posted on 24.01.2007 on this list) So far, i'm getting: Warning: atom names in ../test_min_deflated26_sol_ions.top and ../toto_min_formd.gro don't match (HW2 - HW1) (more than 20 non-matching atom names) WARNING 1 [file "../test_min_deflated26_sol_ions.top", line 38]: 23642 non-matching atom names atom names from ../test_min_deflated26_sol_ions.top will be used atom names from ../OR1G1_min_formd.gro will be ignored The mdrun was launched after this grompp input : grompp_lam \ -f mdp/md_Na.mdp \ -p test_min_deflated26_sol_ions.top \ -pp test_min_deflated26_sol_ions_out.top \ -c toto_min_formd.gro \ -o fullmd_ions.tpr \ -po md_Na_out.mdp \ -deshuf fullmd_ions.ndx \ -shuffle \ -sort \ -np 4 I'd like to pursue the dynamics, so far i'm doing: cd test grompp_lam \ -f ../mdp/pr1.mdp \ -p ../test_min_deflated26_sol_ions.top \ -pp test_out.top \ -c ../toto_min_formd.gro \ -t ../fullmd_ions_deshuf.trr \ -e ../fullmd_ions.edr \ -n toto_min_formd.ndx \ -o test.tpr \ -po test_out.mdp \ -np 4 Thanks a lot for your comments/advices. Cheers, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 134 652 891 78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] problem still lies regarding dssp
Hi Sangeeta, Your out dose not say that the programme is really running. Can you try with .trr and .tpr file and see you get something at the bottom of the output like: Reading frame 0 time0.000 Back Off! I just backed up ddQmCBhK to ./#ddQmCBhK.1# Reading frame 20 time 40.000 Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of sangeeta kundu Sent: Mon 12/02/2007 9:55 AM To: Discussion list for GROMACS users Subject: RE: [gmx-users] problem still lies regarding dssp Dear Abu and Mark, You asked me, whether my computer is shared by many, it is not, I think the program was not hanged because while executing do_dssp -v as usual Gromacs output was given, ":-) G R O M A C S (-: GROningen Mixture of Alchemy and Childrens' Stories :-) VERSION 3.3.1 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2006, 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. :-) do_dssp (-: Option Filename Type Description -f traj.xtc InputGeneric trajectory: xtc trr trj gro g96 pdb -s topol.tpr InputStructure+mass(db): tpr tpb tpa gro g96 pdb xml -n index.ndx Input, Opt. Index file -ssdump ssdump.dat Output, Opt. Generic data file -map ss.map Input, Lib. File that maps matrix data to colors -o ss.xpm Output X PixMap compatible matrix file -sc scount.xvg Output xvgr/xmgr file -a area.xpm Output, Opt. X PixMap compatible matrix file -tatotarea.xvg Output, Opt. xvgr/xmgr file -aa averarea.xvg Output, Opt. xvgr/xmgr file Option Type Value Description -- -[no]h bool no Print help info and quit -[no]X bool no Use dialog box GUI to edit command line options -niceint 19 Set the nicelevel -b time 0 First frame (ps) to read from trajectory -e time 0 Last frame (ps) to read from trajectory -dt time 0 Only use frame when t MOD dt = first time (ps) -tu enum ps Time unit: ps, fs, ns, us, ms or s -[no]w bool no View output xvg, xpm, eps and pdb files -[no]xvgr boolyes Add specific codes (legends etc.) in the output xvg files for the xmgrace program -sss string HEBT Secondary structures for structure count " I changed the permission of dsspcmbi and dsspcmbi.exe files , what else I should do? I mean execpt these two files what are the other files that need change of permission now these two files has read, write, and executable permission, Mark suggested me to call dssp "by hand", will you please explain in more detail?? In order to get taht particular coloured map what procedure should I adopt?? regards SANGEETA "Naser, Md Abu " <[EMAIL PROTECTED]> wrote: Hi Sangeeta, Let me ask you few questions in order to solve the problem. Are you sure your do_dssp prog were running or it was hanged? To make sure please try using verbose output using -v option. Is your computer shared among too many people? What is the file permission status of dssp? To find out use: ls -l /directory/where/you/put/dssp If you see any restricton to file permission change it to chmod a+rx dssp Hope this will help. Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of sangeeta kundu Sent: Fri 09/02/2007 10:13 AM To: gmx-users@gromacs.org Subject: [gmx-users] problem still lies regarding dssp Dear All, I do not know whether I am interrupting you again and again by asking the same question, but I am helpless , I can not detect my fault, When I run the program DSSP it works fine, but while executing do_dssp or my_dssp (as suggested by Yang) the program seems to be never ending, intermediate files are prepared for some time, but I never got any .xpm files, I can not understand whether my system is not working, or I am making any mistake, but all t
[gmx-users] question about genbox -vdwd
Hi all, I have one question: when I use the "genbox -nmol 300 -ci a.gro -cp b.gro" to insert a.gro into b.gro, for some system it gives good results, while not for others. On the other hand, the -vdwd opinion seems not work. I looked at the code of gmx_genbox.c, but didn't find the reason. From the google, I found the following. The problem is the same as mine. Who has good suggestions? Thanks in advance! === http://www.gromacs.org/pipermail/gmx-users/2004-August/011926.html *The resulting output contains atoms which are too close. The distance *>*between the atoms is sometimes *>*as small as 0.01 nm which is smaller than the vanderwaals radii from the *>*database vdwradii.dat . Not *>*surprisingly, therefore I get errors when I run energy minimization or mdrun. *>* The output keeps repeating the message "tested 0 pairs, removed 0 atoms *>* " as I quote below. I would *>*greatly appreciate if somebody could guide me how to use genbox properly. * genbox isn't that good at randomly placing molecules within a box in cases like this (are some emails in the archive on this). It needs a bit of work. I use an in house program to do it, works out much better. Although I don't have it to give out to anyone, since it is part of a much larger package that does a lot of other things and isn't mine to make available. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] eigenrmsf in COMBINED ESSENTIAL DYNAMICS
Hi Sridhar On 2/8/07, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote: Dear Dr. Tsjerk, Thankyou for the suggession. I am however not clear with the explanation. Did you mention the calculation of variance using the mean projection for the eigenrmsf calculations? Yes. The projections of the two trajectories on the combined eigenvectors are different. But, the eigen rmsf plots with give a residue wise rmsf fluctuations along individual eigenvectors are also same for both the trajectories. This is due to the way the principal components are defined. I suggest you read a statistics textbook on principal component analysis. Definetly the fluctuations along the combined eigen vectors should be different for separate trajectories. By no means. Can you explain in a bit detail? It will help you more to read a text on PCA first. I did give it my best shot before. The main thing that seems to be bothering you is what PCA is doing exactly, with which you do have to note that you're dealing with PCA on a combined data set. To understand that may not be trivial, certainly not without understanding the basic theory from PCA. Cheers, Tsjerk -- 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 don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] problem still lies regarding dssp
Dear Abu and Mark, You asked me, whether my computer is shared by many, it is not, I think the program was not hanged because while executing do_dssp -v as usual Gromacs output was given, ":-) G R O M A C S (-: GROningen Mixture of Alchemy and Childrens' Stories :-) VERSION 3.3.1 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2006, 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. :-) do_dssp (-: Option Filename Type Description -f traj.xtc InputGeneric trajectory: xtc trr trj gro g96 pdb -s topol.tpr InputStructure+mass(db): tpr tpb tpa gro g96 pdb xml -n index.ndx Input, Opt. Index file -ssdump ssdump.dat Output, Opt. Generic data file -map ss.map Input, Lib. File that maps matrix data to colors -o ss.xpm Output X PixMap compatible matrix file -sc scount.xvg Output xvgr/xmgr file -a area.xpm Output, Opt. X PixMap compatible matrix file -tatotarea.xvg Output, Opt. xvgr/xmgr file -aa averarea.xvg Output, Opt. xvgr/xmgr file Option Type Value Description -- -[no]h bool no Print help info and quit -[no]X bool no Use dialog box GUI to edit command line options -niceint 19 Set the nicelevel -b time 0 First frame (ps) to read from trajectory -e time 0 Last frame (ps) to read from trajectory -dt time 0 Only use frame when t MOD dt = first time (ps) -tu enum ps Time unit: ps, fs, ns, us, ms or s -[no]w bool no View output xvg, xpm, eps and pdb files -[no]xvgr boolyes Add specific codes (legends etc.) in the output xvg files for the xmgrace program -sss string HEBT Secondary structures for structure count " I changed the permission of dsspcmbi and dsspcmbi.exe files , what else I should do? I mean execpt these two files what are the other files that need change of permission now these two files has read, write, and executable permission, Mark suggested me to call dssp "by hand", will you please explain in more detail?? In order to get taht particular coloured map what procedure should I adopt?? regards SANGEETA "Naser, Md Abu " <[EMAIL PROTECTED]> wrote: Hi Sangeeta, Let me ask you few questions in order to solve the problem. Are you sure your do_dssp prog were running or it was hanged? To make sure please try using verbose output using -v option. Is your computer shared among too many people? What is the file permission status of dssp? To find out use: ls -l /directory/where/you/put/dssp If you see any restricton to file permission change it to chmod a+rx dssp Hope this will help. Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of sangeeta kundu Sent: Fri 09/02/2007 10:13 AM To: gmx-users@gromacs.org Subject: [gmx-users] problem still lies regarding dssp Dear All, I do not know whether I am interrupting you again and again by asking the same question, but I am helpless , I can not detect my fault, When I run the program DSSP it works fine, but while executing do_dssp or my_dssp (as suggested by Yang) the program seems to be never ending, intermediate files are prepared for some time, but I never got any .xpm files, I can not understand whether my system is not working, or I am making any mistake, but all the other programs of Gromacs like pdb2gmx, editconf , genbox, grompp, mdrun etc are going on successfully, problem lies only in case of dssp, I was suggested by Mark to try dssp independently on a single snapshot extracted from the trajectory, I took the snapshot of the protein after 500ps with the command trjconv -f md.xtc -s md.tpr -o time_500ps.pdb -dump 500 (I think the command is correct, if not I earnestly request you to rectify my mistake), When I ran do_dssp on this single structure I waited for 3 days, but it did not finish and seems to be neverending, then I killed the program, In order to get that particular coloured plot of secondary structure
Re: [gmx-users] Nucleic Acids -- Protonate ?
Instead of using GROMACS forcefield, use the AMBER port from stanford. http://folding.stanford.edu/ffamber/ On 2/12/2007 7:36 AM, Viswanadham Sridhara wrote: Hello, I wanted to perform MD simulation on a DNA structure I found from RCSB.org. After changing C, G, A, T to DCYT, DGUA, DADE and DTHY respectively, I used pdb2gmx to create topology file. It says missing hydrogens, which is obvious and I realized I could not use protonate command as ffgmx2.hdb does not have these residues to be protonated. Is there any other file to add missing hydrogens or Is there any other program which you can use to add missing hydrogens to nucleic acids. The total charge now is -43e, which is quite huge, and I am looking to see electric field effects on the DNA. This will be a lot of charge to neutralize by adding counter-ions, if I ignore hydrogens. Looking foward to your response. Best Regards, Vissu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] loss of information trr xtc
If I understand correctly, only the coordinate information can be saved in .xtc. That means, all other informations, velocity, force, etc, can't be reconverted into .trr again. 2007/2/9, Joern Lenz <[EMAIL PROTECTED]>: hi guys. can anyone tell me if there is a loss of information when i convert a trr file into a less-storage-consuming xtc file ? can i reconevrt the xtc file into trr again and then have no loss of information ? thanks for a very short answer Greetings Joern ___ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
