Thank you sir for your response. I already run conventional MD. Then I
calculate the average dihedral and potential energy. Then I run the aMD
simulation. My system is metallo protein human carbonic anhydrase II in
water. When I set iamd=2 and include the dihedral parameters the system is
stable. But when I put the potential energy parameter the system breaks.
Thanking You
On Mon, Jan 6, 2025 at 5:47 PM Steinbrecher, Thomas <
thomas.steinbrecher.roche.com> wrote:
> Well, based on the one snapshot, I would argue that the simulation
> certainly did not work correctly unless there is some sort of severe
> visualisation artefact going on....
>
> Not knowing anything about your system, or aMD, the first suggestion would
> be to run a regular MD, check that your system behaves as you expect and
> only retry an aMD run when you are sure regular MD works without issues.
>
> In parallel, run a test of your aMD protocol on the simplemost system you
> can come up with, something like ethanol in water or so, to check that that
> behaves reasonably, too..
>
> Kind Regards,
>
> Thomas
>
> On Mon, Jan 6, 2025 at 10:46 AM Dulal Mondal via AMBER <amber.ambermd.org>
> wrote:
>
>> please response.
>>
>> On Sun, Jan 5, 2025 at 6:09 PM Dulal Mondal <
>> babunmondal.chem.kgpian.iitkgp.ac.in> wrote:
>>
>> >
>> > Dear Experts,
>> > I am trying to run aMD simulation using amber24. I set the following
>> > parameters in the mdin file
>> > iamd=1,
>> > ethreshp=-159511.27,
>> > alphap=8490.88,
>> >
>> > aMD simulation runs properly. But when I visualize the trajectory I see
>> > the following snapshotr of the protein.
>> > Is this correct? If not, what can I do? How do I set the aMD parameter?
>> > --
>> > *With regards,*
>> > *Dulal Mondal,*
>> > *Research Scholar,*
>> > *Department of Chemistry,*
>> > *IIT Kharagpur, Kharagpur 721302.*
>> >
>>
>>
>> --
>> *With regards,*
>> *Dulal Mondal,*
>> *Research Scholar,*
>> *Department of Chemistry,*
>> *IIT Kharagpur, Kharagpur 721302.*
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
> --
> *Dr. Thomas Steinbrecher*
> Principal Scientist CADD
>
> Roche Pharma Research and Early Development
> Roche Innovation Center Basel
> F. Hoffmann-La Roche Ltd
> Bldg. 06/OG07
> Grenzacherstrasse 124
> 4070 Basel
> Switzerland
>
> Phone +41 61 682 1319
> mailto: thomas.steinbrecher.roche.com
>
--
*With regards,*
*Dulal Mondal,*
*Research Scholar,*
*Department of Chemistry,*
*IIT Kharagpur, Kharagpur 721302.*
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Received on Mon Jan 06 2025 - 06:00:02 PST
