[gmx-users] Simulation of polarizable Carbon nanotubes
Justin Lemkul
jalemkul at vt.edu
Tue Mar 24 02:00:42 CET 2015
On 3/23/15 8:59 AM, Jashimuddin Ashraf wrote:
> Thanks again for your reply Dr. Lemkul.
>
> I was wondering about the update regarding publishing the codes. Are the
> codes ready to be published? Actually I could not get my work done and it
> seems I have to wait until the codes/ patch are available.
>
The paper is under review. Until it is accepted, I am not releasing the code
because people won't know how to use it without the paper. I will announce its
availability whenever that happens. I'm sorry I can't give you much more than
that. It's all in the hands of the reviewers at the moment.
-Justin
> Thanks in advance.
>
> On Wed, Mar 4, 2015 at 10:13 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 3/4/15 11:07 AM, Peter Kroon wrote:
>>
>>>
>>>
>>> On 03/04/2015 04:48 PM, Jashimuddin Ashraf wrote:
>>>
>>>> Thanks for your reply Dr.Peter Kroon and Dr. Lemkul. The virtual_sitesn
>>>>
>>> Im not a Dr. yet ;)
>>>
>>>> directive is very helpful in declaring the virtual site positions.
>>>>
>>>> Now, the simulation runs fine in vacuum. But as soon as I solvate the
>>>> system in water, the production MD fails with-
>>>>
>>>> ------------------------------------------------------------
>>>> ------------------------------------------------------------
>>>> ----------------
>>>> .
>>>> .
>>>> .
>>>> MDStep= 91/ 9 EPot: -6.87315918e+02, rmsF: 1.75e+03
>>>> MDStep= 91/10 EPot: -7.87661133e+02, rmsF: 1.44e+03
>>>> MDStep= 91/11 EPot: -8.65109253e+02, rmsF: 1.22e+03
>>>> MDStep= 91/12 EPot: -9.25257446e+02, rmsF: 1.06e+03
>>>> MDStep= 91/13 EPot: -9.72217041e+02, rmsF: 9.53e+02
>>>> MDStep= 91/14 EPot: -1.00904297e+03, rmsF: 8.72e+02
>>>> MDStep= 91/15 EPot: -1.03802905e+03, rmsF: 8.10e+02
>>>> MDStep= 91/16 EPot: -1.06091382e+03, rmsF: 7.61e+02
>>>> MDStep= 91/17 EPot: -1.07902722e+03, rmsF: 7.23e+02
>>>> MDStep= 91/18 EPot: -1.09339343e+03, rmsF: 6.93e+02
>>>> MDStep= 91/19 EPot: -1.10480664e+03, rmsF: 6.70e+02
>>>> step 91: EM did not converge in 20 iterations, RMS force 579.612
>>>> MDStep= 92/ 0 EPot: -1.14934949e+03, rmsF: 7.17e+02
>>>> Segmentation fault (core dumped)
>>>> ------------------------------------------------------------
>>>> ------------------------------------------------------------
>>>> ----------------
>>>>
>>>> I found that at lower value of the polarizability (alpha_zz), the
>>>> simulation goes fine (in water). The simulation also goes well if I
>>>> decrease the charges of the carbon atoms and the shell. But at the values
>>>> of alpha (0.1296 nm^3) and charges of the carbon atoms (0.25e) as the
>>>> paper
>>>> mentioned, the simulation ends with this error.
>>>>
>>>> In your message, you were kind to reply with-
>>>>
>>>> "If your simulation blows up, try analysing the distance between the
>>>> shell and it's parent; it should give you a hint about what's going
>>>> wrong."
>>>>
>>>> In my case, the distance between the shell and it's parent goes higher
>>>> with
>>>> the increase of the value of alpha. But I cannot understand what is
>>>> causing
>>>> the system to blow up. It would be very much helpful if you could help me
>>>> with this error.
>>>>
>>> See Justin's answer for an explanation.
>>> As for blowing up: if the shell particle moves from it's parent far
>>> enough to reach a positively charged particle the attraction will become
>>> VERY large, blowing up your system.
>>> Check your exclusion list with the original paper. It could be you need
>>> to exclude more. For example: CHARMM treats drude/shell particles in
>>> such a way that if two atoms are in a 1-4 relationship, their
>>> drude/shell particles are as well. According to GROMACS, these would
>>> have a 1-6 relationship.
>>>
>>>
>> ...all of which are normal nonbonded relationships. Note that our Drude
>> force field does Thole screening for 1-2 and 1-3 interactions (based on the
>> parent atoms, not the Drudes, which in a 1-3 interaction of parent atoms
>> would actually be 1-5 interaction for Drudes without this special
>> classification), but anything beyond that is just "normal."
>>
>> -Justin
>>
>>
>> Good luck!
>>> Peter Kroon
>>>
>>>>
>>>> thanks in advance.
>>>>
>>>> On Mon, Feb 23, 2015 at 6:39 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>
>>>>
>>>>> On 2/23/15 3:47 AM, Peter Kroon wrote:
>>>>>
>>>>> On 02/22/2015 05:33 PM, Jashimuddin Ashraf wrote:
>>>>>>
>>>>>> Thanks for your reply Dr. Lemkul
>>>>>>>
>>>>>>> I changed the bond length to zero in my topology file, forcefield file
>>>>>>> and
>>>>>>> in the n2t file. I also added the [ exclusion] section-
>>>>>>>
>>>>>>> If memory serves, you don't need a bond between a shell particle and
>>>>>> it's "parent"; the polarization directive takes care of it's position.
>>>>>> If you want, you can define a non-interacting connection (bond type 5)
>>>>>> between them.
>>>>>>
>>>>>> This is correct. The [polarization] directive is just another bonded
>>>>> interaction. The value of the force constant is back-calculated from
>>>>> the
>>>>> atomic polarizability, alpha.
>>>>>
>>>>>
>>>>> [ exclusions ]
>>>>>>> ; iatom excluded from interaction with i
>>>>>>> 1 2 3 4 5 6 7 8
>>>>>>> 2 1 3 4 5 6 7 8
>>>>>>> 3 1 2 4 5 6 7 8
>>>>>>> 4 1 2 3 5 6 7 8
>>>>>>> 5 1 2 3 4 6 7 8
>>>>>>> 6 1 2 3 4 5 7 8
>>>>>>> 7 1 2 3 4 5 6
>>>>>>> 8 1 2 3 4 5 6
>>>>>>>
>>>>>>>
>>>>>>> in my topology. But the same error keeps showing up. What did I
>>>>>>> possibly
>>>>>>> do
>>>>>>> wrong?
>>>>>>>
>>>>>>> AFAIK this will exclude all atoms from eachother. Just the last line
>>>>>> should be enough if you just want to exclude the shell-carbon
>>>>>> interactions
>>>>>>
>>>>>> In your mail, you were kind to reply with-
>>>>>>>
>>>>>>> "I only looked at the paper briefly, but it seems they are working
>>>>>>> with a
>>>>>>> model that makes use of anisotropic polarization. In GROMACS, this is
>>>>>>> currently only available for water, so the model would not be
>>>>>>> supported."
>>>>>>>
>>>>>>> Are you suggesting that, this model is something we should not work
>>>>>>> with
>>>>>>> in
>>>>>>> GROMACS right now? (I am really sorry, I could not understand this
>>>>>>> part
>>>>>>> properly)
>>>>>>>
>>>>>>> From my quick read of the paper (focusing only a narrow section of
>>>>> the
>>>>> methods), the authors list alpha_zz only, implying that the shell is
>>>>> only
>>>>> polarizable along the normal to the ring. Therefore the other elements
>>>>> of
>>>>> the polarization tensor are zero.
>>>>>
>>>>>
>>>>> Also, it would be very nice, if you could give us an idea about the
>>>>>>> time
>>>>>>> required to publish the codes and adding them in the new versions of
>>>>>>> GROMACS.
>>>>>>>
>>>>>>>
>>>>>>> That depends on reviewers :)
>>>>>
>>>>> The paper should be submitted this week, after which I will be working
>>>>> to
>>>>> submit the code to the master development branch. The code will not be
>>>>> included in 5.1 (I missed the deadline, due to some debugging that took
>>>>> longer than expected), but the code will be available as a patch to the
>>>>> master branch in the coming weeks.
>>>>>
>>>>> -Justin
>>>>>
>>>>>
>>>>> Thanks in advance,
>>>>>
>>>>>> Lastly, for defining the virtual site you could look at the
>>>>>> virtual_sitesn directives and define a center of geometry or a center
>>>>>> of
>>>>>> mass. Im not sure if it has any advantages over a virtual site as it is
>>>>>> defined now though.
>>>>>> If your simulation blows up, try analysing the distance between the
>>>>>> shell and it's parent; it should give you a hint about what's going
>>>>>> wrong.
>>>>>>
>>>>>> Good luck!
>>>>>>
>>>>>> Regards,
>>>>>> Peter Kroon
>>>>>>
>>>>>> On Sat, Feb 21, 2015 at 12:20 AM, Justin Lemkul <jalemkul at vt.edu>
>>>>>>> wrote:
>>>>>>>
>>>>>>>
>>>>>>> On 2/20/15 12:57 PM, Jashimuddin Ashraf wrote:
>>>>>>>>
>>>>>>>> Dear users,
>>>>>>>>
>>>>>>>>> I want to perform a molecular dynamic simulation of polarizable
>>>>>>>>> carbon
>>>>>>>>> nanotubes. I intend to implement this paper-
>>>>>>>>>
>>>>>>>>> http://www.sciencedirect.com/science/article/pii/S0927025607000456
>>>>>>>>>
>>>>>>>>> I digged up the manual but could not find much help from it. I went
>>>>>>>>> through
>>>>>>>>> some mails in the gromacs user maillist, studied some .itp files and
>>>>>>>>> learned some elementary stuffs regarding the addition of virtual
>>>>>>>>> sites
>>>>>>>>> and
>>>>>>>>> shell atoms.I understand that I have to add both shell and virtual
>>>>>>>>> sites
>>>>>>>>> in
>>>>>>>>> this case.
>>>>>>>>>
>>>>>>>>> Now, before jumping right into a big nanotube molecule, I was
>>>>>>>>> trying to
>>>>>>>>> perform a simulation with a single benzene ring with a virtual site
>>>>>>>>> placed
>>>>>>>>> at the center and a shell attached to the virtual site.
>>>>>>>>>
>>>>>>>>> In my forcefield.itp file have the virtual site and the shell
>>>>>>>>> declared
>>>>>>>>> like
>>>>>>>>> this-
>>>>>>>>>
>>>>>>>>> ------------------------------------------------------------
>>>>>>>>> ------------------------------------------------------------
>>>>>>>>> -------------
>>>>>>>>> [ atomtypes ]
>>>>>>>>> ; name mass charge ptype sigma eps
>>>>>>>>> CJ1 1 12.01100 0.25 A 3.40000e-01 3.60100e-01
>>>>>>>>> VS 1 0 0 D 0 0
>>>>>>>>> SL 1 0 -1.5 S 0 0
>>>>>>>>>
>>>>>>>>> [ bondtypes ]
>>>>>>>>> `; i j func b0 kb gamma
>>>>>>>>> CJ1 CJ1 3 0.1418 478.9000 21.867
>>>>>>>>> VS SL 1 0.06 2409
>>>>>>>>> ------------------------------------------------------------
>>>>>>>>> ------------------------------------------------------------
>>>>>>>>> -------------
>>>>>>>>>
>>>>>>>>> Here, I have considered a bond between the virtual site and the
>>>>>>>>> shell
>>>>>>>>> (the
>>>>>>>>> paper mentions something like it but does not provide with the bond
>>>>>>>>> length). Is it a mistake?
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> The equilibrium bond length should be zero (i.e. no induced
>>>>>>>>>
>>>>>>>> polarization).
>>>>>>>>
>>>>>>>> and inside my topol.top file, I have-
>>>>>>>>
>>>>>>>> ------------------------------------------------------------
>>>>>>>>> ------------------------------------------------------------
>>>>>>>>> -------------
>>>>>>>>> [ atoms ]
>>>>>>>>> ; nr type resnr residue atom cgnr charge mass
>>>>>>>>> typeB chargeB massB
>>>>>>>>> 1 CJ1 1 C C 1 0.25
>>>>>>>>> 12.011 ;
>>>>>>>>> qtot 0.25
>>>>>>>>> 2 CJ1 1 C C 1 0.25
>>>>>>>>> 12.011 ;
>>>>>>>>> qtot 0.5
>>>>>>>>> 3 CJ1 1 C C 1 0.25
>>>>>>>>> 12.011 ;
>>>>>>>>> qtot 0.75
>>>>>>>>> 4 CJ1 1 C C 1 0.25
>>>>>>>>> 12.011 ;
>>>>>>>>> qtot 1.00
>>>>>>>>> 5 CJ1 1 C C 1 0.25
>>>>>>>>> 12.011 ;
>>>>>>>>> qtot 1.25
>>>>>>>>> 6 CJ1 1 C C 1 0.25
>>>>>>>>> 12.011 ;
>>>>>>>>> qtot 1.50
>>>>>>>>> 7 VS 1 C VS 1 0 0
>>>>>>>>> ;
>>>>>>>>> qtot 1.50
>>>>>>>>> 8 SL 1 C S 1 -1.5
>>>>>>>>> 0
>>>>>>>>> ;
>>>>>>>>> qtot 0
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> [ polarization ]
>>>>>>>>> ; virtual_site shell functiontype alpha (in nm^3)
>>>>>>>>> 7 8 1 0.1
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> I only looked at the paper briefly, but it seems they are working
>>>>>>>>>
>>>>>>>> with a
>>>>>>>> model that makes use of anisotropic polarization. In GROMACS, this
>>>>>>>> is
>>>>>>>> currently only available for water, so the model would not be
>>>>>>>> supported.
>>>>>>>> It will be soon (I know I've been saying that for a while, but our
>>>>>>>> paper
>>>>>>>> regarding Drude simulations in GROMACS is just about done, after
>>>>>>>> which I
>>>>>>>> can provide the code).
>>>>>>>>
>>>>>>>>
>>>>>>>> [ bonds ]
>>>>>>>>
>>>>>>>>> ; ai aj funct c0 c1 c2
>>>>>>>>> c3
>>>>>>>>> 1 2 3
>>>>>>>>> 1 5 3
>>>>>>>>> 2 4 3
>>>>>>>>> 3 4 3
>>>>>>>>> 3 6 3
>>>>>>>>> 5 6 3
>>>>>>>>> 7 8 1
>>>>>>>>>
>>>>>>>>> [ dihedrals ]
>>>>>>>>> ; ai aj ak al funct c0 c1
>>>>>>>>> c2 c3 c4 c5
>>>>>>>>> 5 1 2 4 3
>>>>>>>>> 2 1 5 6 3
>>>>>>>>> 1 2 4 3 3
>>>>>>>>> 6 3 4 2 3
>>>>>>>>> 4 3 6 5 3
>>>>>>>>> 1 5 6 3 3
>>>>>>>>>
>>>>>>>>> [ virtual_sites3 ]
>>>>>>>>> ; detailed calculation not shown here
>>>>>>>>> ; Dummy from funct a b
>>>>>>>>> 7 4 5 6 1 0.5 0
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> You're missing a critical element here; the paper says that the
>>>>>>>>> shell
>>>>>>>>>
>>>>>>>> does
>>>>>>>> not interact with the carbon atoms of the ring, so you need to define
>>>>>>>> exclusions manually.
>>>>>>>>
>>>>>>>> -Justin
>>>>>>>>
>>>>>>>>
>>>>>>>> ------------------------------------------------------------
>>>>>>>>
>>>>>>>> ------------------------------------------------------------
>>>>>>>>> -------------
>>>>>>>>>
>>>>>>>>> I ran an energy minimization for an emtol of 100 but it gives me a
>>>>>>>>> result
>>>>>>>>> like this-
>>>>>>>>>
>>>>>>>>> Steepest Descents converged to machine precision in 141 steps,
>>>>>>>>> but did not reach the requested Fmax < 100.
>>>>>>>>> Potential Energy = -6.1810545e+06
>>>>>>>>> Maximum force = 9.1656689e+12 on atom 4
>>>>>>>>> Norm of force = 4.5828344e+12
>>>>>>>>>
>>>>>>>>> ------------------------------------------------------------
>>>>>>>>> ------------------------------------------------------------
>>>>>>>>> -------------
>>>>>>>>> If I run a production MD with this, the simulation blows up with
>>>>>>>>> this-
>>>>>>>>> MDStep= 40/18 EPot: nan, rmsF: nan
>>>>>>>>> Warning: Only triclinic boxes with the first vector parallel to the
>>>>>>>>> x-axis
>>>>>>>>> and the second vector in the xy-plane are supported.
>>>>>>>>> Box (3x3):
>>>>>>>>> Box[ 0]={ nan, nan, nan}
>>>>>>>>> Box[ 1]={ nan, nan, nan}
>>>>>>>>> Box[ 2]={ nan, nan, nan}
>>>>>>>>> Can not fix pbc.
>>>>>>>>> MDStep= 40/19 EPot: nan, rmsF: nan
>>>>>>>>> step 40: EM did not converge in 20 iterations, RMS force nan
>>>>>>>>>
>>>>>>>>> ------------------------------------------------------------
>>>>>>>>> ------------------------------------------------------------
>>>>>>>>> -------------
>>>>>>>>> Is something wrong with my system itself? or is there anything wrong
>>>>>>>>> with
>>>>>>>>> my methods?
>>>>>>>>>
>>>>>>>>> I have been stuck at this for a very long time now and anything- any
>>>>>>>>> comment or hint would be very much helpful for me.
>>>>>>>>>
>>>>>>>>> Thanks in advance,
>>>>>>>>> Jashimuddin Ashraf
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>>
>>>>>>>> ==================================================
>>>>>>>>
>>>>>>>> Justin A. Lemkul, Ph.D.
>>>>>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>>>>>
>>>>>>>> Department of Pharmaceutical Sciences
>>>>>>>> School of Pharmacy
>>>>>>>> Health Sciences Facility II, Room 629
>>>>>>>> University of Maryland, Baltimore
>>>>>>>> 20 Penn St.
>>>>>>>> Baltimore, MD 21201
>>>>>>>>
>>>>>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>>>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>>>>>
>>>>>>>> ==================================================
>>>>>>>> --
>>>>>>>> Gromacs Users mailing list
>>>>>>>>
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>>>>>>>> Support/Mailing_Lists/GMX-Users_List before posting!
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>>>>>>>> or
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>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>> ==================================================
>>>>>
>>>>> Justin A. Lemkul, Ph.D.
>>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>>
>>>>> Department of Pharmaceutical Sciences
>>>>> School of Pharmacy
>>>>> Health Sciences Facility II, Room 629
>>>>> University of Maryland, Baltimore
>>>>> 20 Penn St.
>>>>> Baltimore, MD 21201
>>>>>
>>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>>
>>>>> ==================================================
>>>>> --
>>>>> Gromacs Users mailing list
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>>>
>>>
>>>
>>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/
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--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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