From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Apr 11 2016 - 10:08:14 CDT
colvarsTrajFrequency and colvarsRestartFrequency have reasonable default
values, which you can change you like, after reading the documentation.
Clearly RMSD and radius of gyration can never be negative, and
lowerwallconstant is meaningless there.
Note also that the two are intrinsically limited by the finite length of
your molecule, so I would not introduce an upper wall constant either,
unless you really want to confine the simulation to stay close to the (0,
0) state. Just set an upper boundary high enough that the values will
always fit, or turn expandBoundaries on for both variables.
Also, you seem to have mixed sections of different files, since you refer
to variables phi and psi that aren't there.
Giacomo
On Sat, Apr 9, 2016 at 3:53 PM, Sourav Ray <souravray90_at_gmail.com> wrote:
> Also, is it appropriate to consider the backbone or certain central atoms
> for radius of gyration variation or shall we consider all the atoms on the
> peptide chain?
>
> On Sat, Apr 9, 2016 at 10:41 PM, Sourav Ray <souravray90_at_gmail.com> wrote:
>
>> I am planning to run a metadynamics simulation to test the stability of a
>> coarse-grained peptide/protein quartet. It would be really helpful if
>> someone can give me a feedback regarding the COLVARS file I have written.
>>
>> I actually don't understand the correlation between colvarsTrajFrequency
>> and colvarsRestartFrequency with the simulation run time (as in how these
>> relate with the chosen simulation time step). Also, can anyone suggest
>> typical upper and lower wallconstants to be used for gyration and rmsd
>> calculations?
>>
>>
>>
>> colvarsTrajFrequency 500
>> colvarsRestartFrequency 500
>>
>> colvar {
>> name RMSD
>> width 0.1 #Check again
>> lowerboundary 0.0
>> upperboundary 50.0
>> lowerwallconstant 100.0
>> upperwallconstant 100.0
>> outputAppliedForce on
>>
>> rmsd {
>> atoms {
>> atomsfile rmsd_pos.pdb
>> atomsCol B
>> atomsColValue 100.00
>> }
>> refPositionsFile rmsd_ref.pdb
>> refPositionsCol B
>> refPositionsColValue 100.00
>> }
>>
>> }
>>
>> colvar {
>> name GYRA
>> width 0.1 #Check again
>> lowerboundary 0.0
>> upperboundary 50.0
>> lowerwallconstant 100.0
>> upperwallconstant 100.0
>> outputAppliedForce on
>>
>> rmsd {
>> atoms {
>> atomsfile rgyr_pos.pdb
>> atomsCol B
>> atomsColValue 100.00
>> }
>> refPositionsFile rgyr_ref.pdb
>> refPositionsCol B
>> refPositionsColValue 100.00
>> }
>>
>> }
>>
>> metadynamics {
>> colvars phi psi
>> hillWidth 2
>> }
>>
>>
>> Thanks and regards
>> Sourav
>>
>
>
-- Giacomo Fiorin Assistant Professor of Research Institute for Computational Molecular Science (ICMS) College of Science and Technology, Temple University 1925 North 12th Street (035-07), Room 704D Philadelphia, PA 19122-1801 Phone: +1-215-204-4213 Scholar: http://goo.gl/Q3TBQU Personal: http://giacomofiorin.github.io/ Lab page: https://icms.cst.temple.edu/members.html *"As computer programmers we have a responsibility to make sure that we run the computers instead of the computers running us."* - Steve Oualline
This archive was generated by hypermail 2.1.6 : Tue Dec 27 2016 - 23:22:00 CST