AMBER Archive (2006)

Subject: Re: Re: AMBER: A question about Dynamics.

From: Qingning Shu (qshu_at_mail.rx.uga.edu)
Date: Thu Sep 21 2006 - 09:38:47 CDT

Dear sir:
Thank you for your reply. But I checked the .in files again. There is no problem. And I found that even the temperatureVs.time plot had a drop. Following is the two .in files. Thank you.

SHU

md0.in
 &cntrl
  IREST=0, NTX=1,
  igb=1, NTPR=200, NTWX=200,
  ntt=3, gamma_ln=1.0,
  NTR=1, TEMPI=0.0,
  NTB=0,
  TEMP0=300.0,
  NTP=0,
  NSTLIM=100000, DT=0.0005,
  NTC=2, NTF=2,
  CUT=999.0, rgbmax=999,
 &end
Restraint
5.00
RES 1 58
RES 62 266
RES 268 293
RES 295 312
RES 333 354
RES 359 375
RES 380 401
RES 407 431
RES 434 506
END
END

md1.in
 &cntrl
  IREST=1, NTX=7,
  NTR=1,
  igb=1, NTPR=200, NTWX=200,
  ntt=3, gamma_ln=1.0,
  TEMPI=300.0,
  NTB=0,
  TEMP0=300.0,
  NTP=0,
  NSTLIM=100000, DT=0.001,
  NTC=2, NTF=2,
  CUT=999.0, rgbmax=999,
 &end
Restraint
5.00
RES 1 58
RES 62 266
RES 268 293
RES 295 312
RES 333 354
RES 359 375
RES 380 401
RES 407 431
RES 434 506
END
END

-----Original Message-----
From: "David A. Case" <case_at_scripps.edu>
To: amber_at_scripps.edu
Date: Mon, 18 Sep 2006 13:55:47 -0700
Subject: Re: AMBER: A question about Dynamics.

On Mon, Sep 18, 2006, Qingning Shu wrote:

> I have a question about dynamics. I have a system. In Equilibration step I
> used cartesian restraint on the residues that are far away from active site.
> What shuold I do in the production MD, maintain the restraint or remove it?
> I thought I should keep it and ran the preoduction MD with the restraint.
> But I found in the potential-Vs-time plot the potential energy suddenly
> dropped at the beginning point of production MD. In other words, the
> potential energy was not continuous at that point.

Of course, the code itself has no idea what you mean by "equilibration" or
"production". So, if there is a sudden big drop in energy from one part of the
simulation to the next, something probably has changed. Your posting
indicates that the restraints did not change, so you need to look carefully
to see what *did* change. With a discontinous potential energy, it may be
that you didn't really start one part of the simulation from the end point of
the previous one. You should therefore double-check your file assignments and
so on.

...good luck...dac

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