Re: AMBER: Problem with anisotropic pressure scaling

From: David A. Case <>
Date: Fri, 16 Mar 2007 08:55:51 -0700

On Fri, Mar 16, 2007, Linda Prengaman wrote:
> I am trying to do a constant pressure MD run on a DMPC lipid bilayer. I
> would like to set ntp=2, as that seems more appropriate for membrane
> simulations.

I think you will need to change the code to make this work correctly for
bilayer simulations. I don't know if anyone has much experience with bilayer
simulations in Amber -- it would be good if they could post their experiences
and recommendations. I think this is in fact a fairly simple problem to fix,
but it's rather like the weather....

> Unit 5 Error on OPEN:

This message means that the system could not find (or didn't have permissions
to open) the input file. It has nothing to do with the contents of the file.

> The exact same job with ntp=1 runs with no error message.
> Here is the input file in question:
> &cntrl
> nstlim=100000,
> imin=0,nscm=1000,
> nmropt=0,
> ntx=1,irest=0,ntrx=1,
> ntxo=1,ntpr=500,ntwr=500,ntwx=500,ntwv=0,ntwe=0,iwrap=1,
> ntf=2,ntc=2,dt=0.002,
> scnb=8.0,scee=1.2,
> cut=12,ntb=2,
> ntp=2,taup=0.2,pres0=1.0,plevel=2,
> ntt=1,temp0=100,tempi=3,ig=3455476,tautp=1.0
> &end
> Lipid Constraints
> 100.0
> ATOM 1 5888

Note that it is generally not a good idea to run constant pressure at low
temperature...equlibrate the system to the final temperature using constant
volume, *then* turn on constant pressure. Using cut=12 is way overkill, a
value of 8 or 9 should be fine.


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Received on Sun Mar 18 2007 - 06:07:32 PDT
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