Re: [AMBER] Ptraj for diffusion coefficient of water

From: case <>
Date: Sat, 22 Jan 2011 10:03:22 -0500

On Fri, Jan 21, 2011, Ganesh Kamath wrote:
> I used NAMD to run a box of 901 molecules of water using TIP3P model. I used
> tleap to generate a for 901 molecules
> and using TIP3P model. I tried using ptraj to read the namd file using the
> as parm file to compute the diffusion coefficient of
> water at 298 K I get 3.01*10-5 cm2/sec. which is incorrect.

Was any thermostat or barostat used for the NAMD simulation? That would
make the simulation suspect for calculating time-dependent properties.

Also, were the snapshots in namd indeed saved at 1 ps intervals?


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Received on Sat Jan 22 2011 - 07:30:04 PST
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