Re: [AMBER] Solvent Box Wrapping Issue

From: David A Case <case.biomaps.rutgers.edu>
Date: Sun, 22 Feb 2015 16:12:35 -0500

On Sat, Feb 21, 2015, Zhang, Sixue wrote:
>
> Yes, you are right. Short time may cause problems. In another test, I
> used 50000 steps. It also has the same problem. I found that no matter
> what temperature annealing I used, it always stayed at 300 K. Below is
> an example:
>
> solvent NVT equilibritaion
> &cntrl
> nstlim=640000, dt=0.001, ntpr=1000, ntwr=1000, ntwx=1000, iwrap=1,
> tempi=0, ntt=3, imin=0,
> ntb=1, cut=12.0, ig=-1, ntc=2, ntf=2, gamma_ln=2.0,
> ioutfm=1, ntwv=-1, ntr=1, restraintmask=':1-155', restraint_wt=100.0
> /
> &wt TYPE='TEMP0', restraint_wt=100.0, istep1=0, istep2=10000,
> value1=0, value2=300.0, /

The &wt namelists are only read if nmropt>0, but zero is the default value.
You have to specify nmropt=1 in the &cntrl namelist. (See Section 17.8 of
the Reference Manual.)

...good luck...dac


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Received on Sun Feb 22 2015 - 13:30:03 PST
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