Re: [AMBER] umbrella sampling

From: Elisa Frezza <elisa.frezza.gmail.com>
Date: Wed, 17 Oct 2012 15:16:56 +0200

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
>
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>



-- 
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
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Received on Wed Oct 17 2012 - 06:30:05 PDT
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