[gmx-users] AMP_simulation

[RAHUL SURESH]

Hi

On Thu, May 24, 2018 at 5:31 PM, <niki24 at tezu.ernet.in> wrote:

> Hello,
>
> I have tried doing the Molecular dynamics simulation of AMP using the
> Gromos54a7 forcefield.
>
> ITP parameters for the AMP molecule has been generated using the ATB
> builder. Minimization of the molecule goes on well however while carrying
> out the Nvt theres a segmantation fault resulting in step files.
>

Segmentation fault normally occurs for large system with small memory.  You
can write xtc which is a compresssed trajectory file.
Adding time steps to write the file.

>
> Moreover LINCS warning are shown with bonds that rotated more than 30
> degrees. ihave tried changing lincs parameter and also increasing the step
> size, but still simulation crashes.
>

Lincs warning, as for here without knowing exactly about the system, i
think the error is due to improper minimization.
Minimize properly ir go for double precision method.

>
> Is it suggestible to generate topology for the AMP molecule from the
> available topological parameters of ATP in GROMACS. Or are their any
> source of getting the correct itp paremeters for "AMP".
>

Yeah, not an issue I guess.

>
> Thanks
> Nikita Bora
>

Thanks back

>
>
> * * * D I S C L A I M E R * * *
> This e-mail may contain privileged information and is intended solely for
> the individual named. If you are not the named addressee you should not
> disseminate, distribute or copy this e-mail. Please notify the sender
> immediately by e-mail if you have received this e-mail in error and destroy
> it from your system. Though considerable effort has been made to deliver
> error free e-mail messages but it can not be guaranteed to be secure or
> error-free as information could be intercepted, corrupted, lost, destroyed,
> delayed, or may contain viruses. The recipient must verify the integrity of
> this e-mail message.
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>



-- 
*Regards,*
*Rahul *