Re: [AMBER] umbrella sampling

From: Elisa Frezza <elisa.frezza.gmail.com>
Date: Wed, 17 Oct 2012 16:06:42 +0200

Yes,

when I use ntr or other options I have no problem with pmemd.cuda.

Now I'll try.

Thank you

ELisa

2012/10/17 Ignacio J. General <ijgeneral.gmail.com>

> 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
> >>
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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
> > _______________________________________________
> > 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 - 07:30:07 PDT
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