[gmx-users] How to select Force field
rituraj purohit
riturajpurohit at gmail.com
Sun Aug 30 17:12:19 CEST 2009
Dear Friends,
I am geting following error during pr.mdp
-------
Warning: 1-4 interaction between 11 and 18 at distance 1.301 which is
larger than the 1-4 table size 1.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
---------
I am running following commands.
-----
pdb2gmx -ignh -ff G43a1 -f xxx.pdb -o fws.pdb -p fws.top -water spce
editconf -bt cubic -f fws.pdb -o fws.pdb -d 1
genbox -cp fws.pdb -cs spc216.gro -o fws_b4em.pdb -p fws.top
grompp -f em.mdp -c fws_b4em.pdb -p fws.top -o fws_em.tpr
genion -s fws_em.tpr -o fws_ion.pdb -nname CL- -nn 2 -g fws_ion.log
grompp -f em.mdp -c fws_ion.pdb -p fws.top -o fws_em.tpr
mdrun -v -s fws_em.tpr -o fws_em.trr -c fws_b4pr.pdb -e em.edr -g em.log &
grompp -f pr.mdp -c fws_b4pr.pdb -p fws.top -o pr.tpr -maxwarn 3
mdrun -s pr.tpr -o pr.trr -c fws_b4md.pdb -e pr.edr -g pr.log
------
and my pr.mdp is as follows...
-------
title = FWS
cpp = /usr/bin/cpp
define = -DPOSRES
integrator = md
dt = 0.002 ; ps !
nsteps = 100000 ; total 200.0 ps.
nstcomm = 1
nstxout = 250 ; collect data every 0.5 ps
nstvout = 1000
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
vdwtype = cut-off
rvdw = 1.4
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on
Tcoupl = v-rescale
tau_t = 0.1 0.1
tc-grps = Protein Non-Protein
ref_t = 300 300
; Pressure coupling is on
Pcoupl = parrinello-rahman
Pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
__________________
What is theproblem i am not getting, i gone through old gmx list and i
got their may be problem of force field,
Which force field is suitable for my protein (having two chain & net
charge of -42 e) in water ?
Thanks in advanced :)
On 8/30/09, gmx-users-request at gromacs.org <gmx-users-request at gromacs.org> wrote:
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> 1. Re: How to neutralize net charge of protein and why
> (Justin A. Lemkul)
> 2. GROMACS installation for parallel run (George Tsigaridas)
> 3. Re: GROMACS installation for parallel run (Justin A. Lemkul)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 29 Aug 2009 11:49:30 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] How to neutralize net charge of protein and
> why
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4A994E0A.90606 at vt.edu>
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> Please do not include the text of the digest when composing a message. It
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> rituraj purohit wrote:
> > Dear Friends,
> > During first step of MD (pdb2gmx) I come to know that my protein having
> > net charge -42 e (it has two chain, A and B each having -21 e ).
> > Why neutral system is preferable for further steps of MD & what kind of
> > problem encounter with charged system ?
>
> There are theoretical reasons for not simulating a system with a net charge, but
> more intuitively, life does not exist at net charge. For every positive, there
> is a negative somewhere.
>
> > Should i have to add 21 Na+ to make it neutral, through "genion"?
> >
>
> No, you should add 42 Na+, since your system has a net -42e charge.
>
> -Justin
>
> > Regards,
> > Rituraj
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 2
> Date: Sat, 29 Aug 2009 22:44:47 +0300
> From: "George Tsigaridas" <gtsig at upatras.gr>
> Subject: [gmx-users] GROMACS installation for parallel run
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Message-ID: <BE95395F08B14E24BDDAA130C36DD08D at George>
> Content-Type: text/plain; charset="iso-8859-7"
>
> Hi people
>
> Do you have any suggestions on what options to use in the configure command when installing GROMACS for parallel run? Is it possible to change these options at a later time?
>
> Thank you in advance
>
> George
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> ------------------------------
>
> Message: 3
> Date: Sat, 29 Aug 2009 16:31:01 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] GROMACS installation for parallel run
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4A999005.2070602 at vt.edu>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
>
>
> George Tsigaridas wrote:
> > Hi people
> >
> > Do you have any suggestions on what options to use in the configure
> > command when installing GROMACS for parallel run? Is it possible to
> > change these options at a later time?
> >
>
> Besides --enable-mpi? If you want any specifics for your particular system,
> you'll have to describe what you're working with. And no, you can't go back and
> change things without completely re-installing Gromacs. Once the binaries are
> built, they're built based on the options you specified.
>
> -Justin
>
> > Thank you in advance
> >
> > George
> >
> >
> > ------------------------------------------------------------------------
> >
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> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
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> End of gmx-users Digest, Vol 64, Issue 200
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Regads,
Rituraj
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