AMBER Archive (2008)

Subject: Re: AMBER: hybrid remd imaging

From: Geoff Wood (geoffrey.wood_at_epfl.ch)
Date: Thu Mar 27 2008 - 07:56:30 CDT

Dear Carlos,

I'm not sure if you have been looking at the origin of the imaging
problem but I have done some testing to see what might be the cause.
Firstly, I took the standard test system that comes with the code and
reran it and look at the stripped restart files and they look fine. I
then reran the test examples with the input files that I had been
using (only adjusting the numwaterkeep flag) and found that the
imagining was still correct, in other words my input files are fine.
The only other I thing I can think of is that the size of my system,
which is much larger, may be causing some problems. To look at this,
I again took the test example and increased the numwaterkeep flag from
50 to 350, which is the number I had been using, and reran it with an
adjusted topology file, the results again are fine. Finally, I reran
my job to see if something else along the way had caused the problem
but alas the imaging becomes bogus.
So the origin of the bug is still unclear but my feeling is that it
has something to do with the system size. The reason I believe this
is that in order to run the hybrid remd code I had to recompile amber
with an adjusted parameter size to allow a larger number of water
molecules. This adjustment does not effect the test cases that I
mentioned above because I had rerun them with the code that has the
adjusted parameter in it. Do you have any ideas that I could try to
see why the imaging seems to break down in my case but not in the test
cases?

Thanks in advance.

Dr Geoffrey Wood
Ecole Polytechnique Fédérale de Lausanne
SB - ISIC - LCBC
BCH 4108
CH - 1015 Lausanne

On Mar 24, 2008, at 5:21 PM, Geoff Wood wrote:

> I forgot to mention that I only have one peptide + water.
>
> Thanks
> Geoffrey Wood
> Ecole Polytechnique Fédérale de Lausanne
> SB - ISIC - LCBC
> BCH 4108
> CH - 1015 Lausanne
>
>
>
>
> On Mar 24, 2008, at 4:59 PM, Carlos Simmerling wrote:
>
>> you're right, that doesn't seem to be working correctly.
>> can you send me directly your sander input? also do you have
>> anything else in the system except the 1 peptide and water?
>>
>> On Mon, Mar 24, 2008 at 11:51 AM, Geoff Wood
>> <geoffrey.wood_at_epfl.ch> wrote:
>> Dear Amber Community,
>>
>> I am curious about the imaging done in hybrid remd calculations.
>>
>> If I use ptraj commands (see below) to post process a trajectory
>> then the imaged trajectory looks like what one would expect (see
>> attached picture).
>> However, if I look at the stripped restart file then the imaging
>> seems to be a bit strange (see the other attached picture). Could
>> anyone comment on this?
>>
>>
>> ptraj commands:
>>
>> trajin coords
>> center * mass origin
>> image origin center
>> solvent byname WAT TIP3
>> closest 350 :mask first
>> trajout coords.strip nobox
>>
>> Thanks,
>>
>> Dr Geoffrey Wood
>> Ecole Polytechnique Fédérale de Lausanne
>> SB - ISIC - LCBC
>> BCH 4108
>> CH - 1015 Lausanne
>> <ptrajout.jpeg><sanderRestart.jpeg>
>>
>>
>>
>>
>>
>>
>> --
>> ===================================================================
>> 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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