[gmx-users] energy of each residue??

[Pradeep Kota]

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

Fatal error:
Atom 1 in multiple Energy Mon. groups (1 and 4)

Thanks for your help !
regards,
Kota.

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.
>
> Cheers,
>
> Tsjerk
>
> 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
> energy
> > of a protein. I neutralized my system with 8 chloride ions and then made
> an
> > index file with each residue in a different index group, using
> 'splitres'
> > 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
> system
> > thro genion. but i dont think genion really matters in my case. any
> inputs?
> > 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?
> is
> > there a better way?
> >
> > thanks in advance
> > Kota.
> >
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>
> --
> 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
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