AMBER Archive (2008)

Subject: AMBER: hybrid remd imaging

From: Geoff Wood (geoffrey.wood_at_epfl.ch)
Date: Tue Apr 01 2008 - 02:47:18 CDT

>
> Hi Brent,
>
> So I have done some further testing and found that the imaging code
> in multisander only works for truncated octahedral boxes whereas I
> was using a cubic box. The code centers the protein at (0,0,0) for
> the truncated octahedron, which is also the middle cell and also the
> point where the water imaging is done. For the cubic cell the water
> imaging is done around the (0,0,0) point aswell but this is one of
> the box corners so the protein imaging and the water imaging do not
> coincide. This is why the water tended to be at one end during the
> simulations I was running. I reread the amber 9 manual for Hybrid
> remd and there doesn't seem to be a mention of which cell you should
> use but clearly only the octahedral cell should be employed. This
> may have to be explicitly mentioned somewhere but I'm not sure who
> the appropriate person is to inform.
>
> Geoffrey Wood
> Ecole Polytechnique Fédérale de Lausanne
> SB - ISIC - LCBC
> BCH 4108
> CH - 1015 Lausanne
>
>
>
>
> On Apr 1, 2008, at 8:19 AM, Brent Krueger wrote:
>
>> Dear Dr. Wood,
>>
>> Have you resolved this issue yet? I am going to be doing some
>> similar analysis and am interested in if/how you have solved your
>> problem.
>>
>>
>> Thanks,
>> Brent
>>
>>
>>
>>
>>
>> On Thu, Mar 27, 2008 at 5:56 AM, Geoff Wood <geoffrey.wood_at_epfl.ch>
>> wrote:
>> 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
>>>> ===================================================================
>>>
>>
>>
>>
>>
>> --
>> ________________________________________
>> Brent P. Krueger
>> Associate Professor, Hope College
>> on sabbatical during 2007-08 at
>> The Scripps Research Institute
>> phone: 858 784 2912
>> fax: 858 784 9067
>

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