From: Mihaela Drenscko (quo.physics_at_gmail.com)
Date: Mon Jan 09 2017 - 16:20:34 CST
Hi,
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,
Mihaela
On Sun, Jan 8, 2017 at 6:37 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:
> Hi Mihaela, this is a bug fixed a while ago.
>
> Please update to the latest NAMD.
>
> Giacomo
>
> On Fri, Jan 6, 2017 at 9:24 PM, Mihaela Drenscko <quo.physics_at_gmail.com>
> wrote:
>
>> Hi,
>>
>> 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:
>> /.colvars.metadynamics1.1.state
>> /.colvars.metadynamics1.1.hills
>> These files should read outputwq.metadynamics1.1.state and
>> outputwq.metadynamics1.1.hills, according to:
>>
>> http://www.ks.uiuc.edu/Research/namd/cvs/ug/node58.html#sec:
>> colvarbias_meta
>>
>> 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,
>> Mihaela
>>
>
>
>
> --
> 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>
>
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>
> *"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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