I removed the water molecules located between carbon chains of lipids. Then updated the top file. Should the atom numbers of "nvt.gro" be changed? This is not clear for me. I updated the nvt.gro, Running: grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -n index.ndx -o npt.tpr
but it gives me an error about one of the atoms in index file! Or I am supposed to run mdrun without a new grompp? Sincerely, Shima ----- Original Message ----- From: Justin Lemkul <jalem...@vt.edu> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Monday, August 27, 2012 2:33 PM Subject: Re: [gmx-users] NPT equilibration in KALP15-DPPC On 8/27/12 2:30 AM, Shima Arasteh wrote: > > > Hi, > > After the NPT mdrun, I visulized the npt.gro. > I need to know if this npt.gro is the final result of equilibration? From mdrun -h: "The structure file (-c) contains the coordinates and velocities of the last step." > I see 2,3 water molecules between the lipid chains. Should I remove them? Can > I remove them? Or it's not the step that I can make such a decision? > You can remove them. Update the topology and the number of atoms at the top of the .gro file, then re-equilibrate. -Justin > Thanks in advance. > > Sincerely, > Shima > > > ----- Original Message ----- > From: Justin Lemkul <jalem...@vt.edu> > To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS > users <gmx-users@gromacs.org> > Cc: > Sent: Sunday, August 26, 2012 5:29 PM > Subject: Re: [gmx-users] NPT equilibration in KALP15-DPPC > > > > On 8/26/12 8:54 AM, Shima Arasteh wrote: >> >> >> Hi, >> >> For NPT equilibration of KALP15 in DPPC following the Justin's tutorial, when >> I run the grompp command, I get 4 notes. Is it necessary to pay attention to >> the notes ? Are they notable? >> > > Notes are generally notable, yes ;) Never ignore anything grompp tells you, > that's my rule of thumb. Some messages are less critical than others. The > ones > shown here are quite important. > > These warnings cannot possibly be produced by the .mdp file in the tutorial, > and > they suggest that you are not doing NPT under any sort of stable conditions. > You're using plain cutoffs, no constraints, and attempting to produce NVE, > which > will surely fail. > > -Justin > >> >> NOTE 1 [file npt.mdp]: You are using a cut-off for VdW interactions with NVE, >> for good energy conservation use vdwtype = Shift (possibly with DispCorr) >> >> >> NOTE 2 [file npt.mdp]: You are using a cut-off for electrostatics with NVE, >> for good energy conservation use coulombtype = PME-Switch or >> Reaction-Field-zero >> >> Generated 837 of the 2346 non-bonded parameter combinations Excluding 3 >> bonded neighbours molecule type 'Protein' Excluding 3 bonded neighbours >> molecule type 'DPPC' Excluding 2 bonded neighbours molecule type 'SOL' >> Excluding 1 bonded neighbours molecule type 'CL' >> >> NOTE 3 [file topol.top, line 929]: The bond in molecule-type Protein between >> atoms 4 N and 5 H has an estimated oscillational period of 1.0e-02 ps, which >> is less than 10 times the time step of 1.0e-03 ps. Maybe you forgot to change >> the constraints mdp option. >> >> Number of degrees of freedom in T-Coupling group rest is 33897.00 >> >> NOTE 4 [file npt.mdp]: You are using a plain Coulomb cut-off, which might >> produce artifacts. You might want to consider using PME electrostatics. >> >> >> Reading Coordinates, Velocities and Box size from old trajectory Will read >> whole trajectory Last frame -1 time 100.000 Using frame at t = 100 >> ps Starting time for run is 0 ps Largest charge group radii for Van der >> Waals: 0.239, 0.234 nm Largest charge group radii for Coulomb: 0.239, >> 0.234 nm This run will generate roughly 1 Mb of data >> >> There were 4 notes >> >> Thanks for your suggestions in advance. >> >> Sincerely, Shima >> > -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
