AMBER Archive (2009)

Subject: [AMBER] Irregularity in box during md

From: parul sharma (sharmaparul7373_at_gmail.com)
Date: Tue Feb 10 2009 - 04:35:18 CST

Dear All,

I did minimization of my peptide in tip3p box, and the pdb i am getting is
1000rst (see pdb attached), and then i proceeded with the molecular dynamics
using the following input,

constant volume molecular dynamics, 10.0 cut
&cntrl
 imin = 0, irest = 0, ntx = 1, ntb = 1, cut = 10,
 tempi = 0.0, temp0 = 300.0,
ntc=2, ntf=2,
ntt = 3, gamma_ln = 1.0,
 scee= 1.2, nstlim =250000, dt = 0.002,
 ntpr = 500, ntwx = 500, ntwr = 500, ntwe = 500,
&end

however, when i view the pdb 1001rst (see pdb attached), obtained after
molecular dynamics simulation, it shows distorted distribution of water
molecules around the peptide. I would be very thankful if someone could help
me out with this problem. 

-- 
With Best Regards

Parul Sharma
PhD Student, Durban University of Technology,
Durban,
South Africa

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