From: AYTUG TUNCEL (ATUNCEL_at_KU.EDU.TR)
Date: Thu Nov 30 2006 - 16:59:15 CST
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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