[gmx-users] HREX simulation
Shyno Mathew
sm3334 at columbia.edu
Thu Sep 24 20:42:21 CEST 2015
Dear all,
I have two questions regarding REMD
*1. **Calculating the acceptance ratio. *
I started with a 5ns equilibration for all 32 replicas. Then I am doing the
rest of the experiment as multiple HREX simulations of length 5ns each. I
am appending all the info to the existing files. I notice the log files
only show the empirical transition matrix for the latest run only.
For example, following are parts of the transition matrix at the end of 5ns
and 10 ns replica exchange simulations.
*Parts of transition matrix **after 5ns of HREX*
Repl 1 2 3 4 5
Repl 0.7812 0.2188 0.0000 0.0000 0.0000
Repl 0.2188 0.5660 0.2152 0.0000 0.0000
Repl 0.0000 0.2152 0.5776 0.2072 0.0000
Repl 0.0000 0.0000 0.2072 0.5788 0.2140
*Parts of transition matrix **after 10ns of HREX*
Repl 1 2 3 4 5
Repl 0.7908 0.2092 0.0000 0.0000 0.0000
Repl 0.2092 0.5660 0.2248 0.0000 0.0000
Repl 0.0000 0.2248 0.5560 0.2192 0.0000
Repl 0.0000 0.0000 0.2192 0.5604 0.2204
Now, to determine the acceptance rate for the whole 10ns run I should
average these numbers as shown below?
*Calculated transition matrix for the total 10ns HREX*
Repl 1 2 3 4 5
Repl 0.7860 0.2140 0.0000 0.0000 0.0000
Repl 0.2140 0.5660 0.2200 0.0000 0.0000
Repl 0.0000 0.2200 0.5668 0.2132 0.0000
Repl 0.0000 0.0000 0.2132 0.5696 0.2172
2. To continue the run from the previous simulation I am using the
following approach, Can anyone please confirm this method is correct?
*Create new tpr files*
First rename the old tpr files and then create new tpr files where the run
times are extended by another 5 ns
mv ./topol$i.tpr Itopol$i.tpr
tpbconv_mpi -s Itopol$i.tpr -extend 5000 -o topol$i.tpr
*Perform the simulation using the previous cpt files*
mpirun mdrun_mpi -v -deffnm topol -cpi topol -plumed plumed.dat -multi 32
-replex 1000 -nsteps 2500000 -hrex
thanks in advance for your help,
Shyno
On Wed, Sep 2, 2015 at 11:09 PM, Shyno Mathew <sm3334 at columbia.edu> 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.
>
> 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
>
--
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
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