[gmx-users] Basic Query

[Martin Höfling]

Am Mittwoch, 20. Juni 2007 schrieb priyanka srivastava:

> I am currently involved in doing a lipid-peptide
> simulation under NPAT conditions. The way I have
> applied NPAT condition is as follows:
>
> ref_p                   =  0 1
> compressibility         =  0.0 4.5e-5

with semiisotropic?

> Although while performing analysis it shows that the x
> and y dimensions are constant but still I am not sure
> about the way I have applied NPAT. Could somone please
> tell me the basis behind it?

If i am remembering correctly, this is what above values should do:

first dimension is x-y second one is the z direction. Reference pressure is 1 
for both (obviously makes sense) whereas compressibility set to 0 for x-y 
plane prevents box changes in x and y direction. So only z-direction remains 
for adjusting pressure.

> Another thing is I have used vdwtype: cutoff.
> But my intention is not to use the twin range cutoff
> at all!! In my case rlist = rcoulomb = rvdw, i.e. all
> three are same!! Is this alright? (the coulombtype
>         =  PME)

Sorry, didn't get that part of your question. Can you post relevant parts of 
your mdp and specify it further? Chapter 7 says that parameters for PME are 
fourierspacing and pme_order, rcoulomb should not be used then.

Cheers
	Martin