[gmx-users] energy of each residue??
kotanmd at gmail.com
Tue May 1 14:14:33 CEST 2007
Thanks for the response Tsjerk ! I'm sorry that i haven't included any
information in my prev post.
here's my mdp file.
; User spoel (236)
; Wed Nov 3 17:12:44 1993
; Input file
title = Yo
cpp = /usr/bin/cpp
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 5000 ; total 10 ps.
nstcomm = 1
nstxout = 250
nstvout = 1000
nstfout = 0
nstlog = 100
nstenergy = 100
nstlist = 10
ns_type = grid
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
; Berendsen temperature coupling is on in two groups
Tcoupl = berendsen
tc-grps = Protein SOL Cl
tau_t = 0.1 0.1 0.1
ref_t = 300 300 300
; Energy monitoring
energygrps = Protein SOL Cl Protein_MET_1
energygrps_excl = Protein Protein SOL SOL
; Isotropic pressure coupling is now on
Pcoupl = berendsen
Pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is off at 300 K.
gen_vel = no
gen_temp = 300.0
gen_seed = 173529
i had added the groups to the energy monitoring section of the mdp file. and
the error generated was
Program grompp, VERSION 3.3
Source code file: readir.c, line: 819
Atom 1 in multiple Energy Mon. groups (1 and 4)
Thanks for your help !
On 5/1/07, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> Hi Kota,
> In your .mdp file, under energy_grps, you should list your residues.
> As you didn't give much more information, it's hard to tell why grompp
> bailed out. The error message is usually a good thing to add to a
> mail, and in this case, the .mdp file might be too.
> On 5/1/07, Pradeep Kota <kotanmd at gmail.com> wrote:
> > Dear users,
> > I'm trying to compute the contribution of each residue to the total
> > of a protein. I neutralized my system with 8 chloride ions and then made
> > index file with each residue in a different index group, using
> > via make_ndx. it gave me an index file with atoms of each residue in
> > different index groups. but as all these atoms are again listed in the
> > default index group - Protein, grompp shouts out a fatal error. there
> was a
> > post on the list about index groups being bungled up after taking the
> > thro genion. but i dont think genion really matters in my case. any
> > my idea is to calculate the energy of each residue in a given protein. i
> > wish to run a simulation for 10 ps for that. am i going wrong anywhere?
> > there a better way?
> > thanks in advance
> > Kota.
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read
> > http://www.gromacs.org/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 list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users