From: Kevin C Chan (cchan2242-c_at_my.cityu.edu.hk)
Date: Tue Sep 13 2016 - 23:10:21 CDT
Fiorin,
So how could we explain the first few lines of colvars.traj are all
deviated values? Shouldn't they be unwrapped already during the run? Even
if it measure 63.3 from a wrapped coor, it could never measure another 63.3
from a unwrapped one. So what was it coupling?
In fact, you raised a very good point. I have reported previously problems
with colvars when calculating dihedrals with restarted NAMD auto-wrapping
turned on. I just did not aware it could also be the problem with simple
distance calculations.
Thanks anyway.
Ray,
Thank you for the reminding. I thought "ForceNoPBC yes" would help the PBC
problem.
Many more thanks if other colvars contributors could share your experience!
Regards,
Kevin
On Wed, Sep 14, 2016 at 4:22 AM, Sourav Ray <souravray90_at_gmail.com> wrote:
> Hello
>
> If I may add, it is better to keep the box size large (to accommodate the
> variation in colvar) and specify an upper boundary (in case it can be
> determined) to get reasonable results, else the periodic conditions will
> result in large fluctuations in the output generated.
>
> Regards
> Sourav
>
>
> On Wed, Sep 14, 2016 at 1:46 AM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> wrote:
>
>> Hi Kevin, the wrapping is only done in the file, not in the memory during
>> a run. Thus, any wrapping issue would only arise when the restart file is
>> read by the next run.
>>
>> On Tue, Sep 13, 2016 at 1:27 PM, Tabris Chun Chan <
>> cchan2242-c_at_my.cityu.edu.hk> wrote:
>>
>>> Hi Fiorin, thank you for the hints. However, I am wondering if it is the
>>> case, shouldn't colvars meaure the value after NAMD unwrapping the restart
>>> coordinates? If it is really reading a wrapped value, what will happen when
>>> it couples a wrapped value to the window center during a unwrapped run?
>>> Hard to imagine.
>>>
>>> Many thanks!
>>>
>>> Regards,
>>> Kevin
>>>
>>>
>>> On 14 Sep 2016, 00:24 +0800, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>,
>>> wrote:
>>>
>>> Hello Kevin, try looking into possible PBC wrapping issues. Coordinates
>>> are internally unwrapped during a run, but get wrapped when an output file
>>> (such as a restart is written) and this will affect the next run.
>>>
>>>
>>>
>>> On Tue, Sep 13, 2016 at 12:19 PM, Kevin C Chan <
>>> cchan2242-c_at_my.cityu.edu.hk> wrote:
>>>
>>>> Dear Users,
>>>>
>>>> I am doing umbrella sampling in NAMD with the colvars function. I have
>>>> specify a colvars file like this:
>>>> colvarsTrajFrequency 20
>>>> colvarsRestartFrequency 1000
>>>>
>>>> colvar {
>>>> name ProjectionZ
>>>>
>>>> width 1.0
>>>>
>>>> distanceZ {
>>>> main {
>>>> atomsFile ../main.pdb
>>>> atomsCol B
>>>> atomsColValue 1.0
>>>> }
>>>> ref {
>>>> atomsFile ../ref.pdb
>>>> atomsCol B
>>>> atomsColValue 1.0
>>>> }
>>>> forceNoPBC yes
>>>> }
>>>> }
>>>>
>>>> harmonic {
>>>> colvars ProjectionZ
>>>> centers 59.5
>>>> forceConstant 4.0
>>>> }
>>>>
>>>> Pretty standard. The first three lines of colvars.traj reads:
>>>> 0 5.96855721722479e+01
>>>> 20 5.96916027979287e+01
>>>> 40 5.96942978400560e+01
>>>> Pretty close. The last three lines of colvars.traj reads:
>>>> 499940 5.91646234042935e+01
>>>> 499960 5.91735242021637e+01
>>>> 499980 5.91815463732824e+01
>>>> Also close. Good. However, strange things happen when I restart the
>>>> simulation over and over again from restart.coor, restart.vel and
>>>> restart.xsc files.
>>>> After a few times (~70) of restarts. While the last three lines of
>>>> another colvars.traj reads:
>>>> 606960 5.95480754008586e+01
>>>> 606980 5.95456901525873e+01
>>>> 607000 5.95617980942163e+01
>>>> The first three lines of the next colvars.traj reads:
>>>> 0 6.33546567861433e+01
>>>> 20 6.33540970478523e+01
>>>> 40 6.33519859940328e+01
>>>> which was pretty far away from what I want. Then I can see the colvars
>>>> shifting the value towards 5.95. Then for the next colvars.traj:
>>>> 0 4.86674663226018e+01
>>>> 20 4.86540561800189e+01
>>>> 40 4.86566065988872e+01
>>>>
>>>> There seems to have something wrong with restarting simulations with
>>>> colvars turned on. Anyone has experience on this?
>>>>
>>>> Thanks in advance.
>>>>
>>>> Regards,
>>>> Kevin
>>>> City University of Hong Kong
>>>> ukevi_at_gmx.hk
>>>>
>>>
>>>
>>>
>>> --
>>> Giacomo Fiorin
>>> Associate 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
>>>
>>>
>>>
>>
>>
>> --
>> Giacomo Fiorin
>> Associate 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
>>
>>
>>
>
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