You might want to try to equilibrate with weak restraints, thus ntr=1.
You can also try taup = 2.0 (or higher, see p97 in manual).
Maybe something like this(?):
2ns equilibration
&cntrl
imin = 0, irest = 1, ntx = 7,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
cut = 10, ntr = 1,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 1000000, dt = 0.002,
ntpr = 500, ntwx = 5000, ntwr = 5000,
/
Keep protein fixed with weak restraints
0.5
RES 1 524
END
END
Might be worth a try...
As for the "check COM velocity, temp", it is described more here:
http://archive.ambermd.org/200211/0057.html
L
On Jan 4, 2008 5:06 PM, Pankaj R. Daga <pdaga.olemiss.edu> wrote:
>
>
>
>
> Dear Amber community,
>
>
>
> I am running one equilibration using NTP conditions. During simulation, I am
> observing one message repetitively, mentioning
>
>
>
> "check COM velocity, temp: 0.002756 0.01(Removed)
>
> check COM velocity, temp: 0.002198 0.01(Removed)"
>
>
>
> The simulation runs for few thousand cycles (almost half the way) and then
> stops with no message. Could anyone suggest where am I going wrong?
>
>
>
> I tried to run simulation using keyword "nscm =100", However this keyword
> didn't help. I will like to know if this keyword will make any difference in
> the simulation or not? I also searched in the archives, I could not get the
> solution for the problem. Here is the input file.
>
>
>
> Equilibration Run
>
> &cntrl
>
> imin=0,
>
> irest=1,
>
> ntx=7,
>
> ntb = 2,
>
> ntp = 1
>
> ntr=0,
>
> ntc=2,
>
> ntf=2,
>
> tempi=300.00,
>
> temp0=300.00,
>
> ntt=3,
>
> gamma_ln=1.0,
>
> nstlim = 200000, dt= 0.002,
>
> ntpr =2000,
>
> ntwx = 5000,
>
> ntwr = 5000,
>
> cut = 10
>
> /
>
> END
>
>
>
> I will be thankful to you if you could suggest me the way out from this
> situation.
>
>
>
> Thanks and Regards
>
>
>
> Pankaj
>
>
>
> ===============================================================
> If your ship doesn't come in, swim out to it...Jonathan Winters
> ===============================================================
> Pankaj R. Daga |
> Dept. of Medicinal Chemistry | e-mail: pdaga_at_olemiss.edu
> 417 Faser Hall, | fax: +1-662-915-5638
> University of Mississippi | phone: +1-662-915-1853
> University, MS, 38677-1848 |
> ===============================================================
>
>
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Received on Sat Jan 05 2008 - 00:03:41 PST
