[gmx-users] Re: gmx-users Digest, Vol 59, Issue 136

Justin A. Lemkul jalemkul at vt.edu
Thu Mar 19 13:10:28 CET 2009

Pawan Kumar wrote:
> 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.

If your system is not properly energy-minimized, there is no change in dt that 
will help you.  Ensure that your EM converged to reasonable values of Epot and 
Fmax before continuing.

> 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.

These parameters depend upon the force field you are using.  Read about the 
parameter set, as well as modifications that may be made to it.  Studies have 
suggested that longer cut-off's should be used with membrane proteins.  There is 
no substitute for a thorough literature search before starting a project!

> One last question is how to overcome the lincs warnings in position 
> restraint mdrun.

That will depend upon whether or not your system is properly constructed and 


> 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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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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