AMBER Archive (2008)

Subject: Re: AMBER: problem with minimization

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Aug 07 2008 - 10:29:10 CDT

even if you minimize, you might not fix all problems. really high
energies can lead to chirality inversions,
bonds being caught inside rings, and so on. you should look at your
structure very carefully and examine
all parts to make sure there are no problems before minimizing. you
might want to try using cluster analysis
to extract a structure rather than using the average. and average
might be ok to look at, or use as a reference,
but not often ok for running simulations. this is especially true of
the structure is moving while you calculate
the average. you did do a best-fit during the averaging, right? even
then I would not use one as a start for MD.
carlos

On Thu, Aug 7, 2008 at 11:13 AM, <luzhenw1_at_msu.edu> wrote:
> Dear all:
>
> I have a problem when try to do energy minimization of an average
> structure of MD trajectory. Here is the error message:
>
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> rank 1 in job 23 msunmr6_33508 caused collective abort of all ranks
> exit status of rank 1: return code 174
>
> for the output, it stops at the first step:
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 NaN NaN 8.1543E+17 HD22 3787
>
> BOND = 461855.0703 ANGLE = 197335.8187 DIHED =
> 8488.8753
> VDWAALS = NaN EEL = NaN HBOND =
> 0.0000
> 1-4 VDW = ************* 1-4 EEL = 25910.9799 RESTRAINT =
> 0.0000
>
> the input file is simple:
>
> &cntrl
> imin=1, maxcyc=2500,
> ncyc=1000, ntb=0,
> ntr=0,
> cut=12,
>
>
>
> I tried both gas phase and explicit solvent model and failed. the
> result shown here is for gas phase.
>
> it is noticed that the average structure have some clash due to
> average. I think this might have something to do with the error. However, I
> don't know how to deal with it and finish the minimization. Any suggestions
> are welcome. Thanks in advance. please let me know if further information is
> necessary for you.
>
>
>
> 

-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
CMM Bldg, Room G80
Stony Brook University E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
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