[gmx-users] computing electric field for triclinic system

[Fakhar Alam]

>>* I have a small problem with Gromacs, mainly with doing radius of gyration
*>>* calculations, it is all ok with doing the calcualtion, and the command is
*>>* fine but my problem is with the units in which the calculation is
*>>* performed. It is in picoseconds(ps) but i would like to have it in
*>>* nanoseconds(ns) as it is in many publications. If someone could help me
*>>* with this problem how to change the units or how to modify the command to
*>>* have nanoseconds I would appreciate it. Thanks for all the help*


On Tue, Dec 19, 2017 at 10:48 PM, Fakhar Alam <fakharalamchemistry at gmail.com
> wrote:

> which command line is used for SASA? i am using version 5.1.2
>
> On Tue, Dec 19, 2017 at 9:53 PM, Mariia Savenko <mariiasavenko at gmail.com>
> wrote:
>
>> Dear all,
>> I have system in triclinic box. I'd like to plot a potential map on XY
>> axes
>> for a given Z in triclinic box, i.e. For a fixed value of Z I want to have
>> plot of values in this plane.
>> My system is a periodic "planar" molecule. Scripts using variations of the
>> Ewald summation are mainly intended for orthogonal boxes. I concluded that
>> only script which exists for my purpose is the one used internally by
>> Gromacs. I know that Gromacs converts any triclinic box to a rectangular
>> one. To ensure periodicity Gromacs uses shifted images of the unit cell
>> along the triclinic axis. I'd like to understand how the PME algorithm of
>> Gromacs manages with this issue and if anyone has been doing that.
>> Sincerely,
>> Mariia
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