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<riturajpuro...@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-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-us...@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-us...@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-us...@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 > -- 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@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
