[AMBER] umbrella sampling

From: Elisa Frezza <elisa.frezza.gmail.com>
Date: Wed, 17 Oct 2012 11:32:01 +0200

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 - 03:00:03 PDT
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