Hello Justin Sir,<br><br>Thanks for your reply.<br>I changed the dt value as per the suggestion.<br>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.<br>
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.<br>One last question is how to overcome the lincs warnings in position restraint mdrun.<br>
Thanks in advance.<br><br>Thanking you,<br>Pawan<br><br><div class="gmail_quote">On Thu, Mar 19, 2009 at 5:01 PM, <span dir="ltr"></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Pawan Kumar wrote:<br>
> Hi Xavier sir,<br>
><br>
> Thanks for your valuable reply.<br>
> How can I refine the non-bonded set-up ?<br>
<br>
rlist, rcoulomb, rvdw as well as coulombtype. *Never* use cut-off<br>
electrostatics for a membrane system (or really any other, for that matter).<br>
Your results will be far less accurate than with PME (this is in the literature).<br>
<br>
> And where can I specify the time step to 0.0001 ?<br>
<br>
dt (read the manual).<br>
<br>
-Justin<br>
<br>
> I am new to gromacs.<br>
> Sorry to ask such questions.<br>
><br>
> Thanking you,<br>
> Pawan<br>
><br>
><br>
</blockquote></div><br>