[gmx-users] [Fwd: implicit solvation]

[preetichoudhary at iisermohali.ac.in]

---------------------------- 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
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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.
Also we dont need to do nvt and npt equlibration here.We dont neutralise
our system too.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.

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.

thankyou