VMD-L Mailing List

From: Pratik Narain Srivastava (pratik.narain_at_gmail.com)
Date: Sun Nov 22 2020 - 02:07:30 CST

Just use gromacs analysis tools for RMSD and other basic analysis. For
advanced analysis requiring VMD, I suggest you prepare a new trajectory by
removing water and ions using gmx trjconv. This decreases trajectory size
dramatically but it is problematic if water is required for analysis.

On Thu, Nov 19, 2020 at 9:28 PM Ashar Malik <asharjm_at_gmail.com> wrote:

> If you are in graphics mode, start loading the frames and then disable or
> delete the representation using graphics mode. The overhead required by the
> graphics will be removed. Then when the trajectory is fully loaded recreate
> the representation.
>
> Alternatively use command line/script to load the trajectory which will
> take the same time (almost) as the time required using the steps above.
>
> If your time step and record frequency is too close you can choose to skip
> some frames assuming that it doesn't result in a loss of useful
> information.
>
> Removing waters from a trajectory, if you are only interested in a protein
> will also speed things us as the desolvated trajectory will be much small
> smaller and hence will load faster.
>
> Just some things to think about.
>
>
>
> On Thu, 19 Nov 2020, 11:03 PM Raman Preet Singh, <
> ramanpreetsingh_at_hotmail.com> wrote:
>
>> Dear All,
>>
>> I did a fairly long simulation in Gromacs. The trajectory has 100,000
>> frames. Loading of all frames takes several minutes and the waiting time
>> can be annoying. When I look at RMSD using RMSD Tool while the frames are
>> still loading, it shows RMSD of only those frames which have been loaded
>> till that time.
>>
>> Is there a way to avoid the wait and calculate the RMSD of all frames?
>>
>> Thanks
>>
>> Raman
>>
>>
>> 

-- 
Pratik Narain Srivastava,
c/o Dr. Satish Mishra
SRF, LSN-204
MPI division,
CSIR-CDRI, Lucknow
Ph. 9454285924