[gmx-users] g_rdf & more than 8 graph edges
Hi all I encounter a "Fatal error: More than 8 graph edges per atom" when using g_rdf on a trajectory that was generated using 'pbc=full'. pbc=full circumvents this problem in mdrun. I have seen one entry regarding this on may 2006 and unsolved. Is there any news regarding this? thanks Chiradip Chiradip Chatterjee Post Doctoral Research Associate Department of Chemistry and Biochemistry University of California, Santa Barabara USA Phone:1-805-6859381 Mobile :1-805-637-7995 E-mail:[EMAIL PROTECTED] [EMAIL PROTECTED] Home Page: www.chem.ucsb.edu/~cchatterjee/ Group home page : www.chem.ucsb.edu/~gerig/ I LOVE KOLKATA ___ New Yahoo! Mail is the ultimate force in competitive emailing. Find out more at the Yahoo! Mail Championships. Plus: play games and win prizes. http://uk.rd.yahoo.com/evt=44106/*http://mail.yahoo.net/uk ___ 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] g_rdf & more than 8 graph edges
Hi all I encounter a "Fatal error: More than 8 graph edges per atom" when using g_rdf on a trajectory that was generated using 'pbc=full'. pbc=full circumvents this problem in mdrun. I have seen one entry regarding this on may 2006 and unsolved. Is there any news regarding this? thanks Chiradip Chiradip Chatterjee Post Doctoral Research Associate Department of Chemistry and Biochemistry University of California, Santa Barabara USA Phone:1-805-6859381 Mobile :1-805-637-7995 E-mail:[EMAIL PROTECTED] [EMAIL PROTECTED] Home Page: www.chem.ucsb.edu/~cchatterjee/ Group home page : www.chem.ucsb.edu/~gerig/ I LOVE KOLKATA ___ New Yahoo! Mail is the ultimate force in competitive emailing. Find out more at the Yahoo! Mail Championships. Plus: play games and win prizes. http://uk.rd.yahoo.com/evt=44106/*http://mail.yahoo.net/uk ___ 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] Keeping replica numbers consistent when restarting a replica exchange simulation
You may consider modify line 84 to 87
for($k=0; ($k<$nrepl); $k++) {
$order[$k] = $k;
$revorder[$k] = $k;
}
To read in the data in the last line of the previous replica_index.xvg
and replica_temp.xvg.
Regards,
Yang Ye
On 1/27/2007 5:05 AM, Robert Johnson wrote:
Hello everyone,
I'm currently running REMD and using the demux.pl script provided by
David to generate replica_index.xvg and replica_temp.xvg files. I
noticed that each time you restart the simulation (e.g. to extend the
trajectory), all information about the replica index number is lost
and the replicas are renumbered based on the index of their .tpr file.
For example, I am restarting my runs every 1.2 ns. Say that after this
time replica 0 contains the coordinates of replica 42. This will be
evident in the run0_replica_index.xvg file for that particular run.
However, this information is not passed to the subsequent .log files
that provide information about the REMD swaps. Thus, the
run1_replica_index.xvg file will show that replica 0 had the
coordinates of replica 0 at the beginning of run1. Are there existing
scripts that correct for this?
Thanks,
Bob Johnson
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[gmx-users] Keeping replica numbers consistent when restarting a replica exchange simulation
Hello everyone, I'm currently running REMD and using the demux.pl script provided by David to generate replica_index.xvg and replica_temp.xvg files. I noticed that each time you restart the simulation (e.g. to extend the trajectory), all information about the replica index number is lost and the replicas are renumbered based on the index of their .tpr file. For example, I am restarting my runs every 1.2 ns. Say that after this time replica 0 contains the coordinates of replica 42. This will be evident in the run0_replica_index.xvg file for that particular run. However, this information is not passed to the subsequent .log files that provide information about the REMD swaps. Thus, the run1_replica_index.xvg file will show that replica 0 had the coordinates of replica 0 at the beginning of run1. Are there existing scripts that correct for this? Thanks, Bob Johnson ___ 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] g_gyrate
>
> -- Пересланное письмо --
> From: David van der Spoel <[EMAIL PROTECTED]>
> To: Discussion list for GROMACS users
> Date: Fri, 26 Jan 2007 10:02:01 +0100
> Subject: Re: [gmx-users] g_gyrate
> Dmitriy Golubobsky wrote:
> > Dear Gurus,
> > I've got question on Radius of gyrtion calculation.
> > my system consists of 1 polymer and a solvent.
> > I did MD and decide to calculate Rg for this system
> > I made index group consisting my residues
> > g_gyrate -f xtc_file -s tpr_file -n ndx_file -p -o xvg_output
> > ok. I've got the output file with 4 colums: time Rg Rx Ry Rz
> > I use -p option to get components in principal axes, because I' d like
>
> > to calculate form-factors for my system.
> >
> > as I undersand Rg = sqrt ( sum_{i}^{N} r_i*m_i)/M)
> > ok. then fx=Rx/Rg^2, fy=Ry/Rg^2, fz=Rz/Rg^2
> > and I wish to get fx+fy+fz=1 but it is not so.
> > where I'm mistaken?
> > How does components Rxyz in principal axes are calculated?
> > I'm using gromacs 3.3.1
> > Thanks a lot.
> Rg = sqrt ( sum_{i}^{N} (r_i^2)*m_i)/M)
This question can be asked on momet of inertia too.
if I'm calculating moment of ineria in pricipal axes.
is it possible to diagonialize tenzor of inertia? and to get it components?
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Re: [gmx-users] remd and nmr
andrea spitaleri wrote: Hi all, I am trying to perform a REMD simulation on a small cyclic peptide (7 aa). I have calculated a plausible structure by cns using NOEs data leading to 4 clusters with a cutoff of 0.1 nmr and each of them satisfy the NOEs' restraints. However, since it is a small peptide the NOEs could rise from an average of interactions between the few aminoacid and therefore the final structure in one of the existing in solution. Now, I am wondering whether the "quality" of the starting point given to a REMD simulation could in somehow bias the final results. Basically, I am thinking to feed into gromacs one of this structure (the best in procheck_nmr) and to see whether the REMD simulation might explore also the other configurations found by cns and give much more clue on the relative stabilty. Any suggestion? thanks in advance andrea Since you are going to do many replicas you can use all structures and see whether one is favored. You could even use this with restraints on. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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] MPIRUN error while running position restrained MD
Hi Tsjerk, I completely agree with you. I am treating symptoms rather than the problem. I read your previous comment on the LINCS warning to Shangwa Han. I dont have any unnatural amino acids in the protein and EM steps converged to machine precision. I am attaching the potential energy .xvg file after EM. I will look into those atoms and see if I can resolve this problem. Regards, Raghu --- Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote: > Hi Ragothaman, > > You would do good to try and find out what caused > the error. You may > be treating symptoms rather than problems now, and > simply covering up > some more severe wrong in your system. Maybe try to > start a simulation > after some while, using the same parameters as > before. This might > allow your system to relax sufficiently. > > Cheers, > > Tsjerk > > __ Yahoo! India Answers: Share what you know. Learn something new http://in.answers.yahoo.com/ energy.xvg Description: 1113252116-energy.xvg ___ 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] remd and nmr
Hi all, I am trying to perform a REMD simulation on a small cyclic peptide (7 aa). I have calculated a plausible structure by cns using NOEs data leading to 4 clusters with a cutoff of 0.1 nmr and each of them satisfy the NOEs' restraints. However, since it is a small peptide the NOEs could rise from an average of interactions between the few aminoacid and therefore the final structure in one of the existing in solution. Now, I am wondering whether the "quality" of the starting point given to a REMD simulation could in somehow bias the final results. Basically, I am thinking to feed into gromacs one of this structure (the best in procheck_nmr) and to see whether the REMD simulation might explore also the other configurations found by cns and give much more clue on the relative stabilty. Any suggestion? thanks in advance andrea -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ --- ___ 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] Re: gmx-users Digest, Vol 33, Issue 67
-- Пересланное письмо --
From: David van der Spoel <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users
Date: Fri, 26 Jan 2007 10:02:01 +0100
Subject: Re: [gmx-users] g_gyrate
Dmitriy Golubobsky wrote:
> Dear Gurus,
> I've got question on Radius of gyrtion calculation.
> my system consists of 1 polymer and a solvent.
> I did MD and decide to calculate Rg for this system
> I made index group consisting my residues
> g_gyrate -f xtc_file -s tpr_file -n ndx_file -p -o xvg_output
> ok. I've got the output file with 4 colums: time Rg Rx Ry Rz
> I use -p option to get components in principal axes, because I' d like
> to calculate form-factors for my system.
>
> as I undersand Rg = sqrt ( sum_{i}^{N} r_i*m_i)/M)
> ok. then fx=Rx/Rg^2, fy=Ry/Rg^2, fz=Rz/Rg^2
> and I wish to get fx+fy+fz=1 but it is not so.
> where I'm mistaken?
> How does components Rxyz in principal axes are calculated?
> I'm using gromacs 3.3.1
> Thanks a lot.
Rg = sqrt ( sum_{i}^{N} (r_i^2)*m_i)/M)
--
David.
Dear David,
I understand this, thus for the
Rx=Rg = sqrt ( sum_{i}^{N} (x_i^2)*m_i)/M)
and we have to get Rx^2+Ry^2+Rz^2=Rg^2
but we didn't get this.
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Re: [gmx-users] pdbgmx warning long bond
maite lopez a écrit : Dear Gromacs Users, I am trying to simulate a peptide in explicit lipid bilayer membrane environment (say, DPCC). I took well equilibrated dppc.pdb file from Dr. Peter tieleman site and i modified it put in the names of the atoms of the ffG53a5.rtp file . I changed DPPC x DPP in ffG53a5.rtp file. But when executing pdb2gmx ( pdb2gmx_331 -f input.pdb -o output.gro -p output.top -i output.itp -ffG53a5 -water spc -ignh) i 've gived some errors. The long bonds are in the atoms of the membrane. Why it could be? Could anybody give me a pointer to a more elaborated protocol in setting up and running this type of simulation using gromacs? This is my first simulation. I assume you're using Dr. Tieleman's lipids ... The problem comes from the imaging of the lipids, since if you look closely, you'll see some lipids are starting on one side of the box and terminates on the other side. I've explained in detail how to proceed to correct this, please have a look at my message from "30.11.2006 17:57". 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] g_gyrate
Dmitriy Golubobsky wrote:
Dear Gurus,
I've got question on Radius of gyrtion calculation.
my system consists of 1 polymer and a solvent.
I did MD and decide to calculate Rg for this system
I made index group consisting my residues
g_gyrate -f xtc_file -s tpr_file -n ndx_file -p -o xvg_output
ok. I've got the output file with 4 colums: time Rg Rx Ry Rz
I use -p option to get components in principal axes, because I' d like
to calculate form-factors for my system.
as I undersand Rg = sqrt ( sum_{i}^{N} r_i*m_i)/M)
ok. then fx=Rx/Rg^2, fy=Ry/Rg^2, fz=Rz/Rg^2
and I wish to get fx+fy+fz=1 but it is not so.
where I'm mistaken?
How does components Rxyz in principal axes are calculated?
I'm using gromacs 3.3.1
Thanks a lot.
Rg = sqrt ( sum_{i}^{N} (r_i^2)*m_i)/M)
--
David.
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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[gmx-users] g_gyrate
Dear Gurus,
I've got question on Radius of gyrtion calculation.
my system consists of 1 polymer and a solvent.
I did MD and decide to calculate Rg for this system
I made index group consisting my residues
g_gyrate -f xtc_file -s tpr_file -n ndx_file -p -o xvg_output
ok. I've got the output file with 4 colums: time Rg Rx Ry Rz
I use -p option to get components in principal axes, because I' d like to
calculate form-factors for my system.
as I undersand Rg = sqrt ( sum_{i}^{N} r_i*m_i)/M)
ok. then fx=Rx/Rg^2, fy=Ry/Rg^2, fz=Rz/Rg^2
and I wish to get fx+fy+fz=1 but it is not so.
where I'm mistaken?
How does components Rxyz in principal axes are calculated?
I'm using gromacs 3.3.1
Thanks a lot.
--
Dmitriy Golubovsky
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Re: [gmx-users] pdbgmx warning long bond
Hi Maite, The thing is, if pdb2gmx does not encounter a TER statement or chain identifier, it usually tries to bind everything it finds together consecutively. So, you could try to add a number of TER statements, but still, it is better to generate the topology for your protein separately by running it through pdb2gmx and then adding the things together. That will also make your topology much smaller. Tsjerk On 1/25/07, maite lopez <[EMAIL PROTECTED]> wrote: Hi Tsjerk: But, i think the problems is that pdb2gmx program see the membrane how a protein and it tries to tie the peptide with the membrane. The topology of dppc membrane appear in the ffG53a5.rtp file of gromacs. What can i do? Should i create a peptide.top file and include it a lipid.itp and dppc.itp file? The lipid.itp file i took from Dr. Peter tieleman site is for GROMOS87 forcefield and i use GROMOS96 forcefield. Thanks for the help, Maite ___ 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 -- 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
