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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