[gmx-users] HREX simulation
Shyno Mathew
sm3334 at columbia.edu
Fri Sep 25 01:07:10 CEST 2015
Dear Prof. Michael and Prof. Mark,
Thanks so much for your answers, Sorry if I wasn't clear:
1. The end of log file for 5ns HREX (5ns equilibration+5nsHREX) says:
<====== ############### ==>
<==== A V E R A G E S ====>
<== ############### ======>
Statistics over 5000001 steps using 50001 frames
Energies (kJ/mol)
U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14
4.60282e+03 2.72246e+03 2.64238e+02 -5.44737e+02 1.78880e+03
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
1.59850e+04 3.67140e+04 -8.51235e+02 -3.09101e+05 -3.84551e+04
Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
-2.86875e+05 5.49951e+04 -2.31880e+05 2.99998e+02 -1.28397e+02
Pressure (bar) Constr. rmsd
6.82244e-01 0.00000e+00
Box-X Box-Y Box-Z
5.92368e+00 6.22486e+00 5.97121e+00
Total Virial (kJ/mol)
1.84026e+04 1.02972e+01 -1.69321e+01
1.10371e+01 1.82836e+04 1.24158e+01
1.01696e+02 1.05412e+02 1.82995e+04
Pressure (bar)
-1.20301e+01 -2.54959e+00 3.19643e+00
-2.64765e+00 8.90554e+00 -4.28227e-01
-1.47104e+01 -1.44512e+01 5.17129e+00
Epot (kJ/mol) Coul-SR LJ-SR Coul-14 LJ-14
Protein-Protein -8.87422e+03 -3.32093e+03 1.59850e+04 1.78880e+03
Protein-CLA_Water -1.23893e+04 -7.02988e+02 0.00000e+00
0.00000e+00
CLA_Water-CLA_Water -2.87837e+05 4.07379e+04 0.00000e+00
0.00000e+00
T-Protein T-CLA_Water
3.00034e+02 2.99994e+02
Replica exchange statistics
Repl 2500 attempts, 1250 odd, 1250 even
So I guess the energies, box co-ordinates, temperatures are all averaged
over the whole run of 10 ns (5ns equilibration + 5ns HREX).
Now if I compare the log file for the 15ns run (5ns equilibration+ 5ns
HREX+ 5nsHREX),
I see similar information
<====== ############### ==>
<==== A V E R A G E S ====>
<== ############### ======>
Statistics over 7500001 steps using 75001 frames
:
:
:
Replica exchange statistics
Repl 2500 attempts, 1250 odd, 1250 even
If the empirical transition matrix had the information for the whole 10ns
HREX, and considering the exchange interval 1000, the above two lines
should have read the following?
Replica exchange statistics
Repl 5000 attempts, 2500 odd, 2500 even
2. Thanks for your suggestion of using tng file format. I am saving all
my log files before extending each 5ns HREX run.
Can save my output in tng format for gromacs 4.6.7?
3. I only see the Empirical transition matrix in the log files, is there
a way to output the expanded ensemble transition matrix?
Lastly, I know my name is confusing, but I am a she J
Thanks,
Shyno
On Thu, Sep 24, 2015 at 2:42 PM, Shyno Mathew <sm3334 at columbia.edu> wrote:
> 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
>
--
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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