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