On Fri, Mar 15, 2013 at 9:28 AM, <[email protected]> wrote:
> hi, > I am trying to simulate a 50 residue protein in implicit water.Can anyone > tell me that why we usually set the cuttoff to be 0. > See pbc = no in chapter 7. > coulombtype = Cut-off > vdwtype = Cut-off > nstype = grid > nstlist = 0 > rlist = 0 > rcoulomb = 0 > rvdw = 0. > I HAVE SEEN THAT PEOPLE KEEP NO CONSTRAINTS ON THE SYSTEM.Can you explain > why this is being done. > They think that makes for a good model physics for their objective. You need to make a decision here too. See below. > Also we dont need to do nvt and npt equlibration here. You can and should treat some period of time as equilibration. Whether you need to do it in a different call to mdrun is a different question. NPT with no box wouldn't make much sense... > We dont neutralise > our system too. Where would you like the neutralizing atoms to go in your implicit solvent? > But it keeps on showing in note: > NOTE 1 [file topol.top, line 7412]: > System has non-zero total charge: -2.000000 > Total charge should normally be an integer. See > http://www.gromacs.org/Documentation/Floating_Point_Arithmetic > for discussion on how close it should be to an integer. > Check out some textbook material on implicit solvation with the model you're using and see if net charge on the solute is a problem. Likely not. > Correct me if I am wrong. > Also while doing production run,I am getting this error:- > WARNING 1 [file topol.top, line 7412]: > The bond in molecule-type Protein_chain_W between atoms 17 OG and 18 HG > has an estimated oscillational period of 9.0e-03 ps, which is less than 5 > times the time step of 2.0e-03 ps. > Maybe you forgot to change the constraints mdp option. > Like it says, the decisions about using constraints and the size of the time step are linked. See manual 6.7 for introductory discussion. Mark -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
