Re: [AMBER] umbrella sampling

From: Elisa Frezza <elisa.frezza.gmail.com>
Date: Wed, 17 Oct 2012 16:13:55 +0200

Dear Ignacio,

why do you not write &wt type='DUMPFREQ'?

ELisa

2012/10/17 Elisa Frezza <elisa.frezza.gmail.com>

> 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
>> >>
>> >> _______________________________________________
>> >> 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
>>
>> _______________________________________________
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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
>
>
>
>


-- 
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 - 07:30:10 PDT
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