VMD-L Mailing List

From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Mon Oct 19 2015 - 10:59:52 CDT

Hi Bryan and Christopher,

Thanks for this discussion, cleared up some of the doubts I had.

So, to make sure I got this right......I should start by optimizing water
for any atom that should in principle have water interaction, correct? And
then if they are flying out, just not include the log file of those waters
in further calculation, is that what you suggested?

Best regards,
Chitrak.

On Mon, Oct 19, 2015 at 10:50 AM, Mayne, Christopher G <cmayne2_at_illinois.edu
> wrote:

> Bryan,
>
> Apologies for a late reply; I just returned from international travels
> this morning.
>
> Your own suggested answer is quite on target, and it sounds like you have
> a pretty good handle on what is going on at this stage of the
> parameterization.
>
> Regards,
> Christopher Mayne
>
>
> On Oct 19, 2015, at 4:45 PM, Bryan Roessler <roessler_at_uab.edu> wrote:
>
> I'm going to take a stab and try to answer my own question based on some
> further observations.
>
> I believe that it is necessary to remove any waters that do not reach a
> proper minimized state (for instance if they fly out of the Gaussian
> simulation). It is best to try and include as many water interaction target
> files as possible for the fragment (even for atoms that have predefined
> charges), but if some of them skew the optimization results (for instance,
> if they are not near the energy objective in COLP), then it is best to
> reduce their weighting in the calculation or to remove them altogether.
>
> Following these guidelines I have been able to get realistic optimized
> charges near the CGenFF predictions.
>
> If I am in error, please let me know.
>
> Thanks,
>
> Bryan
>
> *Bryan Roessler | Graduate Research Assistant*
> UAB | The University of Alabama at Birmingham
> *uab.edu/cmdb
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__uab.edu_cmdb&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=KWvVUHl42S-_kpj6OunU5-512j104OJKVMt2MxKKoE8&m=e4emalMzSzA_Oigh9_CZfbiAb_QKJDDDcVgTLyiricU&s=kY3pi1-tdUGvhwhTQYeiyWS4EtYsSZq1s6s0caPyp_o&e=>*
> Knowledge that will change your world
>
> On Fri, Oct 16, 2015 at 10:01 AM, Bryan Roessler <roessler_at_uab.edu> wrote:
>
>> Christopher,
>>
>> Thank you very much for the reply. I should have included a second,
>> related question in my original query: since I am not going to include the
>> predefined atoms in the charge optimization step, is it still necessary to
>> calculate the individual water interactions for those atoms and include
>> them as input in the optimization?
>>
>> Because it is necessary to include the known atoms from the bonded
>> residue, the complexity of the fragment also increases (~35 atoms total)--001a113fb92e610b4b0522773c41--