AMBER Archive (2003)

Subject: Re: AMBER: Is NTC=2 correct for minimization when hydrogens are added?

From: Alexey Onufriev (onufriev_at_scripps.edu)
Date: Sat Aug 16 2003 - 11:37:35 CDT

You don't need SHAKE (NTC > 1) for minimization...

                                                Alexey Onufriev

On Sat, 16 Aug 2003, Majid moghaddam wrote:

> Dear all
> I used a pdb file without hydrogens to do MD
> simulations. after loading the pdb file hydrogens are
> added by leap programs. To do minimization before
> starting MD, is it correct to set NTC=2 while in this
> case bonds involving hydrogen are constrained?
> Thanks a lot
> Majid Erfani Moghaddam
>
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