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
>
>
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Received on Mon Mar 20 2017 - 09:30:02 PDT
