[gmx-users] Polymer topology and MD Gromacs

Thu Oct 4 15:13:25 CEST 2018

On 10/1/18 9:25 PM, paul buscemi wrote:
> Alex,
> Thanks for your feedback.
>
> So far the critters seem to be compliant,  align when they should with H bonding, crumple when they should,  and grommp’s major complaint is when I forget to adjust the number of residues. But I am unseasoned in MD and following the discussions on gmx-users you come to realize that there is more to MD than just good looks.  Another set of eyes would do no harm.   I’ll do some more vetting and if the polymers react appropriately in polar and non-polar solvents, I will set it loose.

There are two separate things to be considered: (1) whether your 
procedure works for generating a topology and (2) whether the parameters 
applied are physically valid. I usually have disclaimers in my tutorials 
that the user should not simply assume that my parameters for things are 
correct or necessarily best for any given system, but that the protocol 
itself is robust.

-Justin

>   Best
> Paul
>
>> On Oct 1, 2018, at 1:25 PM, Alex <nedomacho at gmail.com> wrote:
>>
>> I don't really work much with small organics or polymers (angle descriptions should be quite important there), so my review would be at the level of what the good old grumpy robot grompp already does. If you are sure of the parameters and your tests are coming out okay, given some criteria, I say why not share it..
>>
>> Alex
>>
>>
>> On 10/1/2018 11:46 AM, pbuscemi wrote:
>>> Alex, Justin,
>>>
>>> I've managed to make and run polymers using Avogadro ,modifying the n2t, then creating the top using  x2top under  54a7 ff.  The method may be useful for others but before presenting it to the user group,  it  should be reviewed so that  glaring mistakes/concepts are revised.   If you think it worthwhile, would either of you be agreeable to reviewing the process?
>>>
>>> Thanks
>>> Paul
>>>
>>> -----Original Message-----
>>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Alex
>>> Sent: Sunday, September 30, 2018 12:44 AM
>>> To: gmx-users at gromacs.org
>>> Subject: Re: [gmx-users] force field not found
>>>
>>> Yeah, if it is missing bonded parameters, you can always try to find
>>> something similar, at least with OPLS-AA -- don't really know about the
>>> other ff.
>>>
>>> Alex
>>>
>>>
>>> On 9/29/2018 8:58 PM, paul buscemi wrote:
>>>> Alex,
>>>>
>>>> I wanted to practice some more with x2top using  a simple CH3 -( CH2)14 -Ch3  pdb model.  oplsaa works fine, but not 54a7 FF generating the erro  “ cannot find forcefield for C “  Th two CH3’s do not cause the error found but the fourteen CH2’s.
>>>>
>>>> In the ffbonded.itp bond angle types i see CH2-S-CH3  , C-CH2-C and  CH2-S_S, but  not C-CH2-C.  Can I add a new atomas ga 5_55   by anology or hunt for the correct parameters  ? (I’ m trying his now )
>>>>     I am assuming the n2t  nor the rtp do not have to be modified since x2top does not rely on the rtp.  This is a fairly basic but essential task, and would surly like to master it.
>>>>
>>>> Thanks,
>>>> Paul
>>>>
>>>>
>>>>
>>>>
>>>>> On Sep 27, 2018, at 5:47 PM, Alex <nedomacho at gmail.com> wrote:
>>>>>
>>>>> Never dealt with TiO2, but the path to parameterizing forcefields for
>>>>> solid-state structures in MD is becoming more and more straightforward,
>>>>> e.g., J. Phys. Chem. C 2017. 121(16): p. 9022-9031.
>>>>>
>>>>> Alex
>>>>>
>>>>> On Thu, Sep 27, 2018 at 4:11 PM paul buscemi <pbuscemi at q.com> wrote:
>>>>>
>>>>>> Alex,
>>>>>>
>>>>>> There are so many important  reactions / applications in which protein
>>>>>> polymer interactions play a role that  the ability  to generate  of
>>>>>> polymers should be part of gromacs repertoire. I’ll keep plugging away on
>>>>>> this and report to the community if I can break the code  - other than
>>>>>> using the very good but terribly expensive commercial programs.   I would
>>>>>> not doubt that many have already accomplished this this task, but it is not
>>>>>> well tracked within this group.
>>>>>>
>>>>>> I might not approach a Molysulfidnitride substrate , ( making turbine
>>>>>> blades ??)  but TiO2 is indeed another surface very popular with proteins.
>>>>>> Most every nitinol surface is essentially TiO2.  If you have some pointers
>>>>>> on that,  I’m listening.
>>>>>>
>>>>>> Thank you again for the assist.
>>>>>>
>>>>>> Regards
>>>>>> Paul
>>>>>>
>>>>>>
>>>>> -- 
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
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