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-- Jason M. Swails > On Mar 20, 2017, at 12:01 PM, paul <paul_westphaelinger.ewetel.net> wrote: > > hello, > > I was using just one center of mass restraint, both groups containing > three atoms. Both were performed with nmr restraints, and identical > input files. The nvidia-smi outputs I put in the email from before, were > created while I was trying to find out what was going on, so everything > is identical. > > I was using Hamiltonian replica exchange if that helps. If there is more > information I can give you I would be happy to do so. > > This would be an example .in file with the corresponding .disang file : > > the infile: > > &cntrl > ntx=5, > nstlim=1000, > restraint_wt=0.5, > ntr=0, > ntt=3, > temp0=300, > gamma_ln=5.0, > ntc=2, > ntwx=25000, > dt=0.004, > ig=-1, > ntf=2, > cut=9.0, > restraintmask=':1-10', > numexchg=25000, > ntpr=500, > irest=1, > imin=0, > ntxo=2, > nmropt=1, > ioutfm=1, > &end > &wt type='DUMPFREQ', istep1=50,/ > &wt type='END',/ > DUMPAVE=restart0.disang.out > DISANG=restart0.disang > > > the disang file: > > &rst > iat=-1,-1 > iresid=0,irstyp=0,ifvari=0,ninc=0,imult=0,ir6=0,ifntyp=0, > r1=0,r2=11.4,r3=11.4,r4=999, > rk2=5.5,rk3=5.5, > igr1= 29, 62, 94, 127, > igr2= 189, 219, 252, 282, > / > > >> Am 20.03.2017 um 15:44 schrieb David Case: >>> On Mon, Mar 20, 2017, paul wrote: >>> My simulations started crashing and I soon realized that a dramatic >>> increase in memory consumption was at fault. I am using the NMR center >>> of mass distance restraints and after the version change a four window >>> replica system jumped in memory usage. >> Are you using the same inputs, or are you now using "nfe" or something like >> that? Posting your mdin input file + restraints would probably be helpful. >> We would also benefit by knowing how many atoms are involved in the >> center-of-mass calculation. Checking to see what happens if you reduce that >> number might be informative. And, are you using lots of COM restraints, or >> just a few? >> >> What you report does sound like a bug/regression, but we need information >> requested above to even know which routines to look at. >> >> ...thx...dac >> >> >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber >> >> > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Mon Mar 20 2017 - 11:30:03 PDT