From: quo.physics_at_gmail.com
Date: Tue Jan 10 2017 - 05:57:27 CST
Hi,I will update, but it cannot run this lenghty 10 replicas simulations on a regular computer. And what is updated on a supercomputer is for other people to decide.
Anyway, can you please tell me, with the new version, the outputName for each replica is different or is the same? If it is different, does this mean that named will ascribe a name for the combined PMT file, or do I have to do that myself? It is not indicated in the description in which way this procedure is accomplished.
Thank you,Mihaela Sent from my Verizon 4G LTE Smartphone
------ Original message------From: Ajasja Ljubetič Date: Tue, Jan 10, 2017 12:55 AMTo: namd-l;Mihaela Drenscko;Cc: Subject:Re: namd-l: multiple replicas metadynamics
Why not simply update your NAMD version (2.12)? You will get bugfixes and better performance. The updates are free and the installation almost trivial.
Best,Ajasja
On 9 January 2017 at 23:20, Mihaela Drenscko <quo.physics_at_gmail.com> wrote:
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 FiorinAssociate Professor of ResearchInstitute for Computational Molecular Science (ICMS)College of Science and Technology, Temple University1925 North 12th Street (035-07), Room 704DPhiladelphia, 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 thatwe run the computers instead of the computers running us." - Steve Oualline
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