Re: [AMBER] umbrella sampling

From: Ignacio J. General <ijgeneral.gmail.com>
Date: Wed, 17 Oct 2012 10:04:39 -0400

Elisa, I don't see any clear problem in your input, but sometimes even
small details, like one extra or missing space in the input can cause
problems. In particular, I remember that I had a problem once with a
missing space in the restraint file (DISANG file).

Here I copy a pair of input and nmropt restraint files that works for
me, so you can try to copy the format. Hopefully, that will solve the
problem.

Input file:

 &cntrl
   imin = 0,
   irest = 0,
   ntx = 1,
   ntb = 1,
   cut = 10,
   ntp = 0, pres0 = 1.0, taup = 2.0,
   ntt = 3, tempi = 10, temp0 = 298,
   gamma_ln = 2.0, ig = -1,
   ntc = 2, ntf = 2,
   nstlim = 50000, dt = 0.002,
   ntpr = 5000, ntwx = 5000, ntwr = 5000,
   ioutfm = 1,
   nmropt = 1,
 /
&wt type='END', /
DISANG=restraint-distance

Restraint file:

# Restraint on unless bicarbonate distance to two atoms in protein is
less than 3A.
# 1230 BCA C 631 ALA C 5
 &rst
  ixpk= 0, nxpk= 0, iat= 19561, 10245, r1= 1.00, r2= 1.10, r3=3.00, r4=3.50,
      rk2=5.0, rk3=5.0, ir6=1, ialtd=0,
 &end
#
# 1230 BCA C 31 ALA CB 5
 &rst
  ixpk= 0, nxpk= 0, iat= 19560, 534, r1= 1.00, r2= 1.10, r3=3.00, r4=3.50,
&end

Also, I imagine that you have a working installation of pmemd.cuda,
right? Does it work fine with other inputs?

Ignacio


On Wed, Oct 17, 2012 at 9:16 AM, Elisa Frezza <elisa.frezza.gmail.com> wrote:
> Dear Ignacio,
>
> I tried to use only nmropt=1, but I have still the same problem.
> The restraint file is:
>
> &rst iat=243,1001,
> ninc=0,ir6=0,ifntyp=0,nstep1=1,nstep2=90000,
> r1=0.0000E+00,r2=28.0000,r3=28.0000,r4=50.000,rk2=5,rk3=5,ir6=0/
>
> and the output related to this part is:
>
> Begin reading energy term weight changes/NMR restraints
> WEIGHT CHANGES:
> DUMPFREQ 1 0 0.000000 0.000000 0 0
> ** No weight changes given **
>
> RESTRAINTS:
> Requested file redirections:
> DISANG = dist_chi.RST
> DUMPAVE = restraint.log
> Restraints will be read from file: dist_chi.RST
> Here are comments from the DISANG input file:
>
> Number of restraints read = 1
>
> Done reading weight changes/NMR restraints
>
> Thanks you in advance
>
> ELisa
>
> 2012/10/17 Ignacio J. General <ijgeneral.gmail.com>
>
>> Dear Elisa, I have been experimenting with umbrella sampling lately,
>> using GPUs, and I found that it's not possible to use pmemd.cuda with
>> nmropt=1 and ntr=1 at the same time. It just stops, without any clear
>> error message. But this was solved as soon as I changed to use sander
>> (I don't remember now, but maybe it also works fine with pmemd).
>>
>> So, I think your choices are:
>> 1) use sander (or, maybe, pmemd), or
>> 2) use GPUs, but you should try to figure out a way to combine your
>> restraints so that you end up using only nmropt or ntr, but not both.
>>
>> Regards,
>>
>> Ignacio
>>
>> On Wed, Oct 17, 2012 at 5:32 AM, Elisa Frezza <elisa.frezza.gmail.com>
>> wrote:
>> > Dear All,
>> >
>> > I am trying to do umbrella sampling, but the calculation does not run.
>> > I use the following input:
>> >
>> > run: step 1 MD
>> > &cntrl
>> > imin = 0,
>> > irest = 1,
>> > ntx = 5,
>> > nstlim =100000, dt = 0.002,
>> > ntc = 2 , ntf = 2,
>> > ntt = 3, gamma_ln = 2.0,
>> > ntp=1, taup=1,
>> > pres0=1,
>> > tempi = 300.0, temp0 =300.0,
>> > ntb = 2 ,
>> > ntpr = 250 , ntwx = 250, ntwr = 500 ,
>> > cut = 9,
>> > nmropt=1,
>> > restraintmask = :1-48,
>> > restraint_wt=0.0005
>> > /
>> > &wt type='DUMPFREQ', istep1=1 /
>> > &wt type='END' /
>> > DISANG=dist_chi.RST
>> > DUMPAVE=restraint.log
>> >
>> > and the following command:
>> >
>> > cmd="pmemd.cuda.MPI -O -i step11.in -o dimero_step11.out -p
>> > dimero_spce.prmtop -c dimero_step10.rst -r dimero_s
>> > tep11.rst -x dimero_step11.mdcrd -ref dimero_step10.rst"
>> >
>> > In the output file there is not problem, but the calculation is however
>> > aborted:
>> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
>> > Image PC Routine Line
>> Source
>> >
>> > pmemd.cuda.MPI 000000000053FDB0 Unknown Unknown
>> Unknown
>> > pmemd.cuda.MPI 00000000004FF822 Unknown Unknown
>> Unknown
>> > pmemd.cuda.MPI 0000000000433F9E Unknown Unknown
>> Unknown
>> > pmemd.cuda.MPI 0000000000510C80 Unknown Unknown
>> Unknown
>> > pmemd.cuda.MPI 00000000004ECA8B Unknown Unknown
>> Unknown
>> > pmemd.cuda.MPI 000000000040539C Unknown Unknown
>> Unknown
>> > libc.so.6 000000315E01D994 Unknown Unknown
>> Unknown
>> > pmemd.cuda.MPI 00000000004052A9 Unknown Unknown
>> Unknown
>> >
>> >
>> > Can someone help me?
>> >
>> > Thank you in advance
>> >
>> > ELisa
>> >
>> >
>> > --
>> > Elisa Frezza
>> > Ph.D. Student in Materials Science and Engineering
>> > Dipartimento di Scienze Chimiche
>> > UniversitÓ di Padova
>> > via Marzolo, 1
>> > 35131 Padova - Italy
>> > Phone: +39 049 827 5149
>> > Skype: elisa.frezza
>> > Emai: elisa.frezza.gmail.com
>> > elisa.frezza.studenti.unipd.it
>> > _______________________________________________
>> > 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
>>
>
>
>
> --
> Elisa Frezza
> Ph.D. Student in Materials Science and Engineering
> Dipartimento di Scienze Chimiche
> UniversitÓ di Padova
> via Marzolo, 1
> 35131 Padova - Italy
> Phone: +39 049 827 5149
> Skype: elisa.frezza
> Emai: elisa.frezza.gmail.com
> elisa.frezza.studenti.unipd.it
> _______________________________________________
> 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
Received on Wed Oct 17 2012 - 07:30:07 PDT
Custom Search