[gmx-users] [Fwd: implicit solvation]

[Justin Lemkul]

On 3/18/13 1:36 AM, preetichoudhary at iisermohali.ac.in wrote:
>
>
>
> ---------------------------- Original Message ----------------------------
> Subject: implicit solvation
> From:    preetichoudhary at iisermohali.ac.in
> Date:    Fri, March 15, 2013 1:58 pm
> To:      gmx-users at gromacs.org
> --------------------------------------------------------------------------
>
> 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.
> 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.

The choice of whether or not to use constraints comes down to whether you 
believe that a rigid bond or a harmonic one is more appropriate.  What's more, 
constraints allow for larger time steps, and thus more efficient simulations.

> Also we dont need to do nvt and npt equlibration here.We dont neutralise
> our system too.But it keeps on showing in note:

Notes are just informative messages.  They don't necessarily signal that 
anything is wrong (though they can, in some cases).

> 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.
>
> 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.
>

Your time step is too large in the absence of constraints.  For stability and 
energy conservation, you probably have to use a time step of 1 fs or less, 
probably 0.5 fs.

-Justin

-- 
========================================

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

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