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!
Manuel
&cntrl
imin=0,irest=1,ntx=5,ioutfm=1, ntxo=2, nmropt=1
ntb=2,pres0=1.0,ntp=1
taup=2.0,
ntr=0,ntc=2,ntf=2,
tempi=300.0,temp0=300.0,ntt=3,ig=-1,gamma_ln=5, nscm=0
nstlim=1000000,dt=0.002,
ntpr=1000,ntwx=1000,ntwr=10000, isgld=1, tsgavg=1.0, sgft=0.5,
cut=8, iemap=1
/
&ewald
nfft1=64,nfft2=64,nfft3=64
/
&emap
mapfile='cluster2_min4.pdb',atmask=':1-91',fcons=0.02,ifit=1,move=1
/
&emap
mapfile='cluster2_min4.pdb',atmask=':128-401',fcons=0.02,ifit=1,move=1
/
&wt type='DUMPFREQ', istep1=2 /
&wt type='END' /
DISANG=dist_pbc.RST
DUMPAVE=dist_pbc_vs_t
LISTIN=POUT
LISTOUT=POUT
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Received on Thu Jan 08 2015 - 22:00:02 PST
