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-requ...@gromacs.org <gmx-users-requ...@gromacs.org> wrote: > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 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" <jalem...@vt.edu> > Subject: Re: [gmx-users] How to neutralize net charge of protein and > why > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4a994e0a.90...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > Please do not include the text of the digest when composing a message. It > throws off searches of the archives. > > 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" <gt...@upatras.gr> > Subject: [gmx-users] GROMACS installation for parallel run > To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> > Message-ID: <be95395f08b14e24bddaa130c36dd...@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 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20090829/5f492260/attachment-0001.html > > ------------------------------ > > Message: 3 > Date: Sat, 29 Aug 2009 16:31:01 -0400 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] GROMACS installation for parallel run > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4a999005.2070...@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 > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > 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-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- > ======================================== > > 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 > > ======================================== > > > ------------------------------ > > _______________________________________________ > gmx-users mailing list > gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > > End of gmx-users Digest, Vol 64, Issue 200 > ****************************************** > Regads, Rituraj _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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-requ...@gromacs.org. Can't post? 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