Re: [AMBER] sander error "Could not find cntrl namelist"

From: Asmita Gupta <asmita4des.gmail.com>
Date: Tue, 1 Jul 2014 21:52:06 +0530

Okay..i introduced one additional title line and now i am not getting that
message,

I have certain questions regarding setting up mdin file for smd
simulations, though

1. When i changed the cut value from 10 to 12, i got different error
messages e.g

with cut=10, sander terminates with error
=====================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= EXIT CODE: 11
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
=====================================================================================
APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)



with cut=12, it terminates with
=====================================
vlimit exceeded for step 0; vmax = **********
 SANDER BOMB in subroutine nonbond_list
  volume of ucell too big, too many subcells
  list grid memory needs to be reallocated, restart sander
======================================

What Cut off value should i use, because in the prior production run i used
a cut off of 12.0



2. Say i want to pull one end of DNA helix with a velocity of 5m/s, how can
i set that in mdin file? (is it by adjusting nstlim, dt and path)

3. How can i determine the direction of pulling, whether parallel to DNA
helix axis or perpendicular to it?

Being a beginner in SMD, can you plz tell how can i set this information in
mdin file?


Thanks



On Tue, Jul 1, 2014 at 9:10 PM, Jason Swails <jason.swails.gmail.com> wrote:

> On Tue, Jul 1, 2014 at 8:31 AM, Asmita Gupta <asmita4des.gmail.com> wrote:
>
> > Dear users,
> >
> >
> > I am trying to set up an SMD run using this input file (the ncsu_smd
> > section has been taken from the amber tutorial files)
> >
> > &cntrl
> > imin = 0,
> > irest = 1,
> > ntx = 5,
> > ntb = 2,
> > pres0 = 1,
> > ntp = 1,
> > taup = 2.0,
> > cut = 10.0,
> > ntc = 2,
> > ntf = 2,
> > tempi = 300.0,
> > temp0 = 300.0,
> > ntt = 3,
> > ig = -1,
> > ioutfm = 1,
> > iwrap = 1,
> > gamma_ln = 1.0,
> > nstlim = 100000, dt = 0.0005, tol = 0.00001,
> > ntpr = 500, ntwx = 500, ntwr = 5000000
> > /
> > ncsu_smd
> > output_file = 'smd.txt'
> > output_freq = 1000
> >
> > variable
> > type = LCOD
> > i = (8,9,493,494)
> > r = (1.0,-1.0)
> > path = (17.5,50)
> > harm = (100.0)
> > end variable
> > end ncsu_smd
> >
> > =====================
> >
> > but i am getting this error
> >
> > "Could not find cntrl namelist"
> > =============================
> >
> > I did a google search for this error and found that this might be due to
> > certain formatting issues in mdin file.
> >
> > But i can't see any formatting error in the mdin file. Can you pls
> suggest
> > what's wrong in this file?
> >
>
> ‚Äč&cntrl cannot be on the first line of your input file when you are using
> sander. The first line is read as a title and ignored (this is not true
> with pmemd as far as I can tell).
>
> I tested an otherwise valid mdin file setting the &cntrl tag on the first
> line and I got the same error you did.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Jul 01 2014 - 09:30:03 PDT
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