[gmx-users] How to select Force field
Tsjerk Wassenaar
tsjerkw at gmail.com
Sun Aug 30 17:51:04 CEST 2009
Hey :)
What did grompp say (and why -maxwarn 3)? And what did the previous
steps give? Did you check the convergence of the potential energy
during energy minimization? Was there anything odd running pdb2gmx?
Oh, and why would you waste resources using a cubic box?
Tsjerk
On Sun, Aug 30, 2009 at 5:12 PM, rituraj
purohit<riturajpurohit at gmail.com> wrote:
> 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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>> Today's Topics:
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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>
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>>
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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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>
> Regads,
> Rituraj
> _______________________________________________
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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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