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FTSM in STRINGM c41b1 free energy output
#36454 06/21/17 08:06 PM
Joined: Jun 2017
Posts: 1
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JoeP Offline OP
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Hello,

I am rather new to CHARMM. I am interested in using the finite temperature string method (FTSM) in the string method (STRINGM) module of CHARMM version c41b1. I am having a few issues with my output. I am going to attach the install file, output and input I am currently working with for reference. I am running CHARMM on my campus cluster which utilizes XEON E5-2680 processors for Basic and Standard memory configurations.

The goal of this FTSM simulation is to output the final path of a transition for alanine dipeptide between two conformational states in terms of phi/psi coordinates and determine the free energy along this path. What I have noticed is the following:

I get the same exact path regardless of the restraint parameters I set (kpar, kprp, dprp). I have varied these parameters by 3 orders of magnitude each and still gotten the same exact final phi/psi coordinates.
I get output of zeros for the free energy and force output files (attached as .txt). I do not know if this is related to the first issue.

The command I issue on the command line is as follows:
Code:
 mpirun -np 10 $STRINGM -i input/test.inp > output/test.out 


I have looked through documentation regarding this method including the input file (ftsm.inp) included in c40test/ directory and have not been able to come up with a solution to these issues. I have been able to successfully run the test script provided, ftsm.inp, and although the final path was not outputted (my correl command issued errors) the free energy for each image was successfully written to file.

Using ftsm.inp as a guide, I tried adjusting parameters to try and get free energy output but was unsuccessful. The echeck value I used may seem a bit high. I set it to 9999.0 because of an energy tolerance error I received for a simulation with high restraint parameters and 100 images. I tried adding the Hamiltonian replica exchange to my script as well and got the same exact output path and free energies (zeros). I am afraid it may be something I have overlooked.

Please note that I removed the bulk of step update printout in the output file in accordance with 'read before posting'. If I did this in error, please let me know and I would be happy to attach the full output which is rather long. I hope that I have provided adequate information regarding this issue. Thank you for your time.

Best,
Joe P

Attached Files
force_dat.txt (708 Bytes, 124 downloads)
free_energy_dat.txt (238 Bytes, 140 downloads)
test_inp.txt (4.92 KB, 163 downloads)
test_out.txt (105.29 KB, 170 downloads)
stringm_install.txt (896 Bytes, 156 downloads)
Re: FTSM in STRINGM c41b1 free energy output
JoeP #36459 06/23/17 07:48 PM
Joined: Sep 2003
Posts: 8,507
rmv Online Content
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Joined: Sep 2003
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Probably not the best place to start for a new CHARMM user.

You may need to contact the author.


Rick Venable
computational chemist


Moderated by  lennart, rmv 

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