[gmx-users] Doubt regarding membrane protein in POPC bilayer

[Pawan Kumar]

Hello Justin Sir,

Thanks for your reply.
I changed the dt value as per the suggestion.
But after 200 steps the same kind of warnings came  like "pressure scaling
more than 1%" and "1-4 interactions" and then it stopped after writing few
pdb files. Then I decreased the dt value still lesser (0.00001) and this
time it continued with all the given steps but the lipids' structure were
distorted into small fragments.
The other query I have is what should the optimal value for these parameters
for membrane proteins :  rlist, rcoulomb, and rvdw. I have used the value of
1 before.
One last question is how to overcome the lincs warnings in position
restraint mdrun.
Thanks in advance.

Thanking you,
Pawan

On Thu, Mar 19, 2009 at 5:01 PM,

> Pawan Kumar wrote:
> > Hi Xavier sir,
> >
> > Thanks for your valuable reply.
> > How can I refine the non-bonded set-up ?
>
> rlist, rcoulomb, rvdw as well as coulombtype.  *Never* use cut-off
> electrostatics for a membrane system (or really any other, for that
> matter).
> Your results will be far less accurate than with PME (this is in the
> literature).
>
> > And where can I specify the time step to 0.0001 ?
>
> dt (read the manual).
>
> -Justin
>
> > I am new to gromacs.
> > Sorry to ask such questions.
> >
> > Thanking you,
> > Pawan
> >
> >
>
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