[gmx-users] the mdp parameters for localpressure calculation using gromacs-4.0.2_localpressure

[Amit Choubey]

On Fri, Aug 19, 2011 at 8:50 AM, KONG Xian <xianshine at gmail.com> wrote:

> I have sent this email days ago, but I got no answer.****
>
> Hope someone would saw it this time. ****
>
> Sorry for disturbing.****
>
> Dear all:****
>
>          I am using gromacs-4.0.2_localpressure to calculate the local
> pressure of my system.****
>
>          I have a question.****
>
>          When rerun the mdrun from gromacs-4.0.2_localpressure I used a new
> .mdp file. There are some changes of the new .mdp file according the
> original one. I have 2 questions:****
>
> **1.      **I changed the The coulomb interaction type from PME to
> reaction field with epsilon_r=1 epsilon_rf=78;  Is this change feasible?
>
Yes, you have to switch to cutoff for coulomb interaction. I have seen in
other publications that they use a regular coulomb  with cutoff as large as
2 nm. I am not sure whether there is any advantage in using Reaction field.

> ****
>
> **2.      **I used LINCS for all bonds in the simulation, and I still use
> the LINCS for all bonds when calculate the local pressure. Is this way
> right?
>
 I have had no problems in using LINCS during local pressure calculation.

> ****
>
> ** **
>
> Thanks for any reply.****
>
> ** **
>
> Best wishes, ****
>
> KONG Xian****
>
> Tsinghua, Beijing, China****
>
>
>
> ****
>
>
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