Re: [AMBER] umbrella sampling

From: Ignacio J. General <ijgeneral.gmail.com>
Date: Wed, 17 Oct 2012 08:13:19 -0400

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
> _______________________________________________
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Received on Wed Oct 17 2012 - 05:30:03 PDT
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