VMD-L Mailing List

From: xiaoyu qing (xiaoyuqing6601_at_gmail.com)
Date: Sun May 19 2019 - 03:30:07 CDT

Dear VMD users,

I would like to use volutil to divide an EM density may into two equal
parts, what is the command?

Thanks a lot in advance,
Xiaoyu

On Sat, May 18, 2019 at 1:22 AM Peter Freddolino <petefred_at_umich.edu> wrote:

> Dear San,
> This issue had been brought up a little while ago (
> https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/28784.html) - the
> answer is that multithreading in the CPU version was disabled to make it
> compatible with the multilevel summation code. Speaking of that -- unless
> you have a very good reason to be doing this with a brute force
> calculation, things will run much faster if you use multilevel summation
> (add "-m multigrid" to the command line arguments).
> Best,
> Peter
>
> On Fri, May 17, 2019 at 12:29 PM san kumar <ksan93259_at_gmail.com> wrote:
>
>> Dear VMD users,
>>
>> I am using cionize plugin (version 1.0) in the new version of VMD
>> (1.9.4). The capsid net charge is -240e. The calculation is running for 10
>> days and is not still completed. I am using following command:
>>
>> *cionize -i cionize.in <http://cionize.in> -p 4 capsid.pqr*
>>
>> The calculation is not running parallel. Please see the below message:
>>
>> Number of atoms: 915960
>> Number of grid points: 362422340
>> Calculating grid energies...
>> calc_grid_energies_excl_jsthr()
>>
>> *using 1 processors*
>>
>> Any kind of advice/suggestions will be deeply appreciated.
>>
>> Thanks in advance,
>> San
>>
>