Re: RE: water box deformation

Date: Fri Dec 01 2006 - 10:10:15 CST

Well I guess I got the answer. Somehow my parameters are similar to your example. Here are the parameters,

# Periodic Boundary Conditions
cellBasisVector1 106. 0. 0.
cellBasisVector2 0. 117. 0.
cellBasisVector3 0. 0. 90.
cellOrigin 32.0 10.0 50.0
wrapAll on

# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 108
PMEGridSizeY 120
PMEGridSizeZ 90
The differences between the vectors and gridsizes seem to be in an acceptable range. If that is OK, then NPT water equilibration (before the actual run) should be responsible for the deformation, since I did not do in my simulation. But the question is when (before or after minimization) and how long should it be done? I mean is there anyway to understand whether the water molecules reached equilibrium so that I can continue with NVT run. thanks for the reply.


-----Original Message-----
From: "Ana Celia Araujo Vila Verde" <>
To: <>
Date: Thu, 30 Nov 2006 18:15:35 -0500
Subject: RE: namd-l: water box deformation


I didn't quite understand what you said related to PMEGRidSize, but you should definitely equilibrate your molecule in NPT before running in NVT, otherwise the number of water molecules for the volume you're simulating will most likely be wrong (if you want water to have a density around 1 g/cm3) and you'll start observing voids in the water.

The PMEgridSize values may be a little smaller or bigger than the actual values you use for the cellBasisVector but they should always be factorizable (if there is such a word) in 2s, 3s or (less good) 5s to speedup the calculations. Eg:
cellBasisVector1 99.9 0. 0.
cellBasisVector2 0. 99.9 0.
cellBasisVector3 0. 0. 63.

I would use
PME yes
PMEGridSizeX 96
PMEGridSizeY 96
PMEGridSizeZ 64

because 64=2**6 and 96=3 * 2**5

Hope it helps.
Ana Célia Araújo Vila Verde
Penn State University
Department of Chemical Engineering
Fenske Laboratory
University Park, PA 16802
Phone: +(1) (814) 863-2879
Fax: +(1) (814) 865-7846

-----Original Message-----
From: [] On Behalf Of AYTUG TUNCEL
Sent: Thursday, November 30, 2006 5:59 PM
Subject: namd-l: water box deformation

Dear all,

I made explicit solvent simulation (NVT) for my protein. While solvating the molecule I made the box size distance 10 ang. away from the protein. But in the early steps of the run after minimization some deformations occured in the water box. When I load the dcd symmetrical collapse of the water molecules at the sides of the box can easily be seen. I did some mining in the archive and figured that it may related to PMEGridSize values.For x and y axis they are greater than the cellBasisVectors by 2 and 3 ang. respectively. Might this be the only reason for the deformation or are there other factors. Another question is, how can I overcome this problem, should I run a short NPT simulation before the actual run to establish a uniform water distribution (density) in the box? thanks in advance.


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