Hi,
I am trying to simulate a GPCR in POPC bi-layer. The minimization protocol is mainly based on following lipid tutorial link.
http://ambermd.org/tutorials/advanced/tutorial16/An_Amber_Lipid_Force_Field_Tutorial.html
Minimize the lipid structure
&cntrl
imin=1,
maxcyc=10000,
ncyc=5000,
ntb=1,
ntp=0,
ntf=1,
ntc=1,
cut=10.0,
ntpr=50,
ntwr=2000,
&end
/
I'll update you on PMEMD run. However is there way to reduce/ignore non-bonded terms ? Thanks.
Rejwan
________________________________
From: David A Case <case.biomaps.rutgers.edu>
To: Rejwan <rejwan_88.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Monday, August 19, 2013 3:31 PM
Subject: Re: [AMBER] AMBER minimization job
On Mon, Aug 19, 2013, Rejwan wrote:
>
> An AMBER minimization job was aborted due to overflow of non-bonded
> list. My system is of 52 K atoms size. How I can perform minimization
> in such situation ? Thank you.
>
>
> Exit code -5 signaled from c321-214
> * NB pairs 522 1219601 exceeds capacity ( 1219712) 23
> SIZE OF NONBOND LIST = 1219712
Can you post your min_lipid.in file? Also, try a short serial (non-parallel)
run to see if the problem is specific to the parallel code. Trying pmemd
instead of sander is also worth trying, since the nonbond lists are handled
in a different way there.
....dac
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Received on Mon Aug 19 2013 - 13:30:03 PDT
