[gmx-users] HREX simulation

[Shyno Mathew]

Dear all,

I have a very basic question regarding the
<https://contactmonkey.com/api/v1/tracker?cm_session=174703e4-d9a8-42fe-b117-6625d14acb92&cm_type=link&cm_link=3a62973a-0692-4c69-8016-e9f19162d720&cm_destination=http://demux.pl>
demux.pl
<https://contactmonkey.com/api/v1/tracker?cm_session=174703e4-d9a8-42fe-b117-6625d14acb92&cm_type=link&cm_link=9fabcd9d-11de-4873-a28d-2455c9cedc5e&cm_destination=http://demux.pl>
For RMSD calculations, I need to make trajectories that are structurally
continuous. So I copied the script to demux.pl
<https://contactmonkey.com/api/v1/tracker?cm_session=174703e4-d9a8-42fe-b117-6625d14acb92&cm_type=link&cm_link=b95447d6-6ebe-4bc7-afb2-dccc3a114288&cm_destination=http://demux.pl>
to my current directory and replaced line 4 where it says ("Please specify
input filename") with the input filename, for eg:

$in = shift || die("topol0.log");

When I execute "perl demux.pl"
<https://contactmonkey.com/api/v1/tracker?cm_session=174703e4-d9a8-42fe-b117-6625d14acb92&cm_type=link&cm_link=b9e3b425-1110-4dc6-a23e-e5489d4a9cd4&cm_destination=http://demux.pl>
I get the message "topol0.log at
<https://contactmonkey.com/api/v1/tracker?cm_session=174703e4-d9a8-42fe-b117-6625d14acb92&cm_type=link&cm_link=954af1dc-e672-45b3-932c-3fee98049ad3&cm_destination=http://demux.pl/>
demux.pl
<https://contactmonkey.com/api/v1/tracker?cm_session=174703e4-d9a8-42fe-b117-6625d14acb92&cm_type=link&cm_link=69acbc28-8598-4113-bbcd-f2adaa55395a&cm_destination=http://demux.pl>
line
4."

This is the first perl script I am using. I tried different options, still
the script is not running. Can someone help.

thanks so much,
Shyno

On Mon, Aug 31, 2015 at 10:57 AM, Shyno Mathew <sm3334 at columbia.edu> wrote:

> Dear Prof. Shirts, Prof. Abraham,
>
> Thanks so much for the detailed explanation. Sorry for the delay in
> responding, I didn't see the replies till now!
> I did increase the number of replicas, hope to see better results.
>
> have a great day,
> Shyno
>
> On Thu, Aug 27, 2015 at 12:35 PM, Shyno Mathew <sm3334 at columbia.edu>
> wrote:
>
>> Dear all,
>>
>> I am new to doing replica exchange simulations.
>> I am trying to understand the empirical transition matrix printed in the
>> log files. I tried exchange intervals 2 ps and 0.2 ps. However, later I
>> read gromacs recommends exchange interval not to be under 1ps. The system
>> is protein in water and I am only showing parts of the matrix:
>>
>> Exchange interval: 0.2 ps
>> Repl            1            2            3            4             5
>>
>> Repl  0.9528  0.0472  0.0000  0.0000  0.0000
>> Repl  0.0472  0.9017  0.0511  0.0000  0.0000
>> Repl  0.0000  0.0511  0.8946  0.0543  0.0000
>> Repl  0.0000  0.0000  0.0543  0.8898  0.0558
>>
>> 1. If I look at line 3 ""Repl  0.0472  0.9017  0.0511" does this mean
>> exchange between replica 1, 2 is accepted 4.72 %  and exchange between 2,3
>> is accepted 5.11 % ?
>>
>> Repl            1            2            3            4             5
>>
>>
>> Repl  0.9504  0.0496   0.0000  0.0000  0.0000
>>
>> Repl  0.0496  0.8982  0.0522   0.0000  0.0000
>>
>> Repl  0.0000  0.0522  0.8942  0.0536   0.0000
>>
>> Repl  0.0000  0.0000  0.0536  0.8888  0.0576
>>
>> 2. With exchange interval 2 ps, I am getting slightly better acceptance
>> rate. For example, again looking at line 3 "Repl  0.0496  0.8982  0.0522"
>> the acceptance rate for exchange 1 to 2 is 4.96 %, and he acceptance
>> rate for exchange 2 to 3 is 5.22 %
>>
>> thanks,
>> Shyno
>>
>>
>> --
>> Shyno Mathew
>> PhD Candidate
>> Department of Chemical Engineering
>> Graduate Assistant
>> Office of Graduate Student Affairs
>> The Fu Foundation School Of Engineering and Applied Science
>> Columbia University
>>
>
>
>
> --
> Shyno Mathew
> PhD Candidate
> Department of Chemical Engineering
> Graduate Assistant
> Office of Graduate Student Affairs
> The Fu Foundation School Of Engineering and Applied Science
> Columbia University
>



-- 
Shyno Mathew
PhD Candidate
Department of Chemical Engineering
Graduate Assistant
Office of Graduate Student Affairs
The Fu Foundation School Of Engineering and Applied Science
Columbia University