[gmx-users] implicit solvation

[Mark Abraham]

On Fri, Mar 15, 2013 at 9:28 AM, <preetichoudhary at iisermohali.ac.in> 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