From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Mon Jan 09 2017 - 23:55:38 CST
Why not simply update
NAMD version (2.12)? You will get bugfixes and better performance. The
updates are free and the installation almost trivial.
On 9 January 2017 at 23:20, Mihaela Drenscko <quo.physics_at_gmail.com> wrote:
> By the way, the namd version I was using so far was 2.10.So for the
> multiple replica metadynamics, when naming all replicas outputs with one
> common name, say r (instead of giving individual names as 1, 2, 3...10): I
> get these errors:
> ERROR: Error on renaming file r.restart.coor to r.restart.coor.old: No
> such file or directory
> FATAL ERROR: Unable to open binary file r.restart.coor: File exists
> So if I give the same name to each replica, I get this error; if I give
> different names, the 10 pmfs (for 10 replicas) don't combine to one pmf
> file. What, then is the way out?
> Thank you,
> On Sun, Jan 8, 2017 at 6:37 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
>> Hi Mihaela, this is a bug fixed a while ago.
>> Please update to the latest NAMD.
>> On Fri, Jan 6, 2017 at 9:24 PM, Mihaela Drenscko <quo.physics_at_gmail.com>
>>> When I run namd with multiple replicas metadynamics, I don't get files
>>> outputwq.colvars.name.replicaID.state and outputwq.colvars.name.replicaId.hills,
>>> where outputwq is the name of each outputName. Instead, the paths of these
>>> file are written in a file called metadynamics1.outputwq.files, text:
>>> These files should read outputwq.metadynamics1.1.state and
>>> outputwq.metadynamics1.1.hills, according to:
>>> So these files can't be read by other replicas and pmfs can't be combine
>>> into one. All i get are partila pmf, from each replica.
>>> Any suggestions, what is wrong? Why .state and .hills files are not
>>> written with outputName prefixes, without the need foe their paths to be
>>> written in afile?
>>> Thank you,
>> 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 <(215)%20204-4213>
>> 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
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