Dear Amber developers and users,
It seems the Molecular Virial is the 3d stress/pressure tensor matrix.
However, my system is a cubic box, and the output shows that the
stress/pressure tensor matrix is not symmetric. I found in Amber Manual
that when ncsm is applied to a periodic system, it only remove the
translational COM motion, but not the rotational COM motion. I wonder if my
understanding is correct. And if my understanding is right, I wonder if the
way to get a symmetric pressure tensor is by adding the matrix with its
transpose, and then divided by 2?
Thank you very much!
Best,
Mo
On Fri, Oct 26, 2012 at 9:57 PM, Mo Chen <mc842.cornell.edu> wrote:
> Dr. Walker,
> Thank you very much! I tried that, and the output contains a lot of
> virials. May I ask if the "MOLECULAR VIRIAL" might be the pressure tensor?
> Below is some of the output when verbose=2.
>
> NET FORCE PER ATOM: 0.4415E-05 0.1952E-05 0.2797E-05
>
> Evdw = -2031.744615774814
> Ehbond = 0.000000000000
> Ecoulomb = -14495.492337471656
>
>
> Iso virial = 216.227026086809
> Eevir vs. Ecoulomb = 0.000242820370
>
> E electrostatic (self) = -15975.164926588330
> (rec) = 122.536452334002
> (dir) = -6887.433383591240
> (adj) = 8244.569520373911
>
> MOLECULAR VIRIAL: 0.29231825E+03 -.29915649E+03 -.83210699E+02
> MOLECULAR VIRIAL: -.61735342E+02 -.28922154E+03 -.46530167E+03
> MOLECULAR VIRIAL: -.30846131E+02 0.15143719E+03 0.21313031E+03
>
> Best,
> Mo
>
>
> On Fri, Oct 26, 2012 at 7:48 PM, Ross Walker <ross.rosswalker.co.uk>wrote:
>
>> Hi Mo,
>>
>> Try adding the following after the cntrl name list
>>
>>
>> &cntrl
>> ..
>> ..
>> /
>> &ewald
>> verbose=1,
>> /
>>
>> There are 3 verbosity settings (1,2 and 3) which print more and more info
>> about the PME calculation. I can't remember if this prints info about the
>> pressure tensor or not. It might so try it quickly and see what you get.
>>
>> All the best
>> Ross
>>
>> /\
>> \/
>> |\oss Walker
>>
>> ---------------------------------------------------------
>> | Assistant Research Professor |
>> | San Diego Supercomputer Center |
>> | Adjunct Assistant Professor |
>> | Dept. of Chemistry and Biochemistry |
>> | University of California San Diego |
>> | NVIDIA Fellow |
>> | http://www.rosswalker.co.uk | http://www.wmd-lab.org |
>> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
>> ---------------------------------------------------------
>>
>> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
>> be read every day, and should not be used for urgent or sensitive issues.
>>
>>
>>
>>
>>
>>
>>
>> On 10/26/12 3:57 PM, "Mo Chen" <mc842.cornell.edu> wrote:
>>
>> >Dear Amber users and developers,
>> >I would like to write out the pressure tensor through the NPT
>> simulations.
>> >I have found some inquiries about this on the Internet in 2009, which
>> said
>> >the pressure tensor could be printed if we edited the runmd.f file, but I
>> >am not sure how exactly this could be done. I appreciate it if anyone
>> >could
>> >help me with it. Thank you!
>> >
>> >Best,
>> >Mo
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>>
>>
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>
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Received on Mon Oct 29 2012 - 00:30:02 PDT
