RE: water box deformation

From: Ana Celia Araujo Vila Verde (
Date: Thu Nov 30 2006 - 17:15:35 CST


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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