Re: [AMBER] Using restraints to get a complex

From: <>
Date: Fri, 9 Jan 2015 13:56:14 +0800 (CST)

Thanks for the suggestions. What I meant by "nothing happens" is that the simulation with or without the EMAP constraints resulted in secondary structure being completely destroyed. When I checked my trajectory output, the emap energies were given as 0.
Since then, I've checked the test files, and have used the input file from the emap2 test as a basis for mine (see below). This results in EMAP values of around -4500, which sounds much better.
The main difference between the two systems, I think, is that I wasn't originally using SG-langevin dynamics (only langevin thermostatization). That leads me to my next question. From what I read in the manual, I understood that SG-langevin was optional (recommended for large conformational changes) but not absolutely necessary. Am I mistaken in the way I read it? Does that mean that EMAP constraints cannot be used with GPU acceleration?
Although, as I mentioned in a previous post, I have found a way to solve my problems which does not entail EMAP constraints for this particular setup, I am very interested in using them in other systems.
Thanks very much!
  imin=0,irest=1,ntx=5,ioutfm=1, ntxo=2, nmropt=1
  tempi=300.0,temp0=300.0,ntt=3,ig=-1,gamma_ln=5, nscm=0
  ntpr=1000,ntwx=1000,ntwr=10000, isgld=1, tsgavg=1.0, sgft=0.5,
  cut=8, iemap=1
 &wt type='DUMPFREQ', istep1=2 /
 &wt type='END' /

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Received on Thu Jan 08 2015 - 22:00:02 PST
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