[gmx-users] Basic Query

[priyanka srivastava]

Hie,

Many thanks for your reply.

Yes I have used semi-isotropic coupling.

Another doubt is why only a value of 4.5e-5?

I have used PME and have mentioned rcoulomb in the
.mdp file too, which as is pointed out by you, has no
meaning!! But does this mean that my mdp file is
wrong? Because if PME does not use rcoulomb it shud
simply ignore the value.
Actually I do not want to use twin range cutoff. So, I
have given rvdw = rlist. Is this alright?
Portion of my mdp file looks like this:

; Electrostatics
coulombtype             =  PME
fourier_nx              =  6.4
fourier_ny              =  5.0
fourier_nz              =  8.1
pme_order               =  4
rcoulomb                =  1.5
rvdw                    =  1.5

Also since I have not specified "vdwtype" in the mdp
file, so it automatically takes Cut-off.

regards,
Pri...


--- Martin Höfling <martin.hoefling at gmx.de> wrote:

> 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
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the
> list. Use the 
> www interface or send it to
> gmx-users-request at gromacs.org.
> Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
> 



       
____________________________________________________________________________________
Pinpoint customers who are looking for what you sell. 
http://searchmarketing.yahoo.com/