AMBER Archive (2009)

Subject: Re: [AMBER] input file / skinnb

From: Mag. Thomas Taylor (thomas.taylor_at_univie.ac.at)
Date: Wed Sep 16 2009 - 02:49:32 CDT

On Thursday 10 September 2009 13:03:17 Carlos Simmerling wrote:
> the best way to troubleshoot input errors in cases like this is to delete
> one line at a time until it works.

Finally I got it to work, by the modus operandi you suggested.

Anyway as it turns out the skinnb parameter leads to "error in reading
namelist cntrl". The same script without it at least gets a simulation going.
According to 2.7.2 in the Amber10 Manual it should work/exist and is even
claimed as recommended for all PME runs.

Has anybody successfully used the skinnb parameter?

Thank you,
Thomas

PS: Just in case, here is the script I use:

EMIM TRIF 50: 100ps slice
 &cntrl
 imin = 0,
 igb = 0,
 irest = 0,
 ntx = 1,
 ntb = 1,
 iwrap = 1,
 cut = 10.0,
> skinnb = 4.0,
 ipol = 0,
 ntpr = 1000,
 ntwr = 0,
 ntc = 2,
 ntf = 2,
 ntt = 3,
 gamma_ln = 1.0,
 tempi = 300.0,
 temp0 = 300.0,
 dt = 0.002,
 nstlim = 50000,
 nscm = 5000,
 ntwx = 50,
 ntwv = 0,
 ioutfm = 1
 /
> error in reading namelist cntrl

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