Or is there a way to set up the input file so that the rotational motion is
removed at the same frequency as the translational motion?
Best,
Mo
On Mon, Oct 29, 2012 at 3:04 AM, Mo Chen <mc842.cornell.edu> wrote:
> 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
>>> >_______________________________________________
>>> >AMBER mailing list
>>> >AMBER.ambermd.org
>>> >http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>>
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>>
>>
>
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Received on Mon Oct 29 2012 - 00:30:03 PDT
