[gmx-users] HREX simulation

[Justin Lemkul]

On 9/2/15 11:09 PM, Shyno Mathew wrote:
> 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.
>

Don't modify the script.  The input .log file is the argument read from the 
command line.  The "die" statement just means "if there is not input file given, 
print this message," hence what's happening to you.

-Justin

> 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
>>
>
>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================