From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Tue May 17 2016 - 14:44:52 CDT
Yup, this isn't a colvars issue, I think it may have to do with the recent
alchemy improvements by Brian Radak. Let me CC him to get his attention...
:-)
Jerome
On 17 May 2016 at 21:20, Reza Salari <resal81_at_gmail.com> wrote:
> Hi Giacomo,
>
> I repeated my test simulation without colvars and it seems that the
> problem still persists. I provided more info here:
> https://gist.github.com/resal81/250d65964d72dd85759a26e8b9bb0a20
>
> Reza
>
> =========================================
> Reza Salari, M.D. Ph.D.
> Postdoctoral Researcher
> Center for Computational and Integrative Biology
> Rutgers University
> Science Building
> Camden, NJ 08102
> (856) 225-6492
> =========================================
>
> On Mon, May 16, 2016 at 7:51 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> wrote:
>
>> Hi Reza can you post the complete output of NAMD (including colvars
>> output)?
>>
>> The error could come from the latest NAMD, the latest colvars snapshot
>> (not merged into NAMD yet), or by an interaction between the two.
>>
>> Although you probably want to keep the colvars restraints to continue
>> your production run, it may also be a good idea to disable colvars and see
>> if this will gives a consistent behavior between NAMD 2.11 and CVS.
>>
>> Giacomo
>> On May 16, 2016 5:30 PM, "Reza Salari" <resal81_at_gmail.com> wrote:
>>
>>> Hi,
>>>
>>> I'm running some FEP tests on Stampede using the development versions of
>>> NAMD and Colvars (from CVS and github, respectively) and noticed very large
>>> dE_avg (and subsequently dG) values in the fepout files:
>>>
>>> STEP Elec vdW
>>> dE dE_avg Temp dG
>>> # l l+dl l
>>> l+dl E(l+dl)-E(l)
>>> #NEW FEP WINDOW: LAMBDA SET TO 0.89 LAMBDA2 0.9
>>> FepEnergy: 50 -172948.7128 -172948.7462 3821.4453
>>> 3822.1917 0.7129 -36458.2406 300.2047 -9999999999.9999
>>> FepEnergy: 100 -172545.4504 -172545.4839 3375.0287
>>> 3375.7949 0.7328 -36445.1885 301.0309 -9999999999.9999
>>> FepEnergy: 150 -173167.4969 -173167.5303 3786.2865
>>> 3786.9088 0.5888 -36445.1217 302.0768 -9999999999.9999
>>> FepEnergy: 200 -172776.3445 -172776.3780 3466.1294
>>> 3466.9678 0.8050 -36458.5775 301.4277 -9999999999.9999
>>> FepEnergy: 250 -172866.1536 -172866.1870 3604.4608
>>> 3605.2236 0.7293 -36456.9526 300.7179 -9999999999.9999
>>>
>>> The compile script is attached at the end. I think this is a bug -
>>> possibly because dE_avg is not initially set to the dE value of the first
>>> step. In the meantime the dG values are recoverable by using dE and Temp
>>> directly.
>>>
>>> Best Regards,
>>> Reza Salari
>>>
>>> #===================================================
>>> *System*: Stampede
>>>
>>> *Loaded modules:*
>>>
>>> $ module list
>>> 1) intel/15.0.2 2) mvapich2/2.1 3) xalt/0.6 4) TACC
>>>
>>>
>>> #===================================================
>>> #!/usr/bin/env bash
>>>
>>> set -e
>>>
>>> NAMD_VERSION="2016-05-09"
>>>
>>> download_namd () {
>>> wget
>>> http://www.ks.uiuc.edu/Research/namd/cvs/download/741376/NAMD_CVS-${NAMD_VERSION}_Source.tar.gz
>>> tar xzf NAMD_CVS-${NAMD_VERSION}_Source.tar.gz
>>> ln -s NAMD_CVS-${NAMD_VERSION}_Source namd_cvs
>>> }
>>>
>>> download_colvars () {
>>> wget https://github.com/colvars/colvars/archive/master.zip
>>> unzip master.zip
>>> ln -s colvars-master colvars
>>> }
>>>
>>> download_fftw_tcl () {
>>> cd namd_cvs
>>>
>>> wget
>>> http://www.ks.uiuc.edu/Research/namd/libraries/fftw-linux-x86_64.tar.gz
>>> tar xzf fftw-linux-x86_64.tar.gz
>>> ln -s linux-x86_64 fftw
>>>
>>> wget
>>> http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.5.9-linux-x86_64.tar.gz
>>> tar xzf tcl8.5.9-linux-x86_64.tar.gz
>>> ln -s tcl8.5.9-linux-x86_64 tcl
>>>
>>> wget
>>> http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.5.9-linux-x86_64-threaded.tar.gz
>>> tar xzf tcl8.5.9-linux-x86_64-threaded.tar.gz
>>> ln -s tcl8.5.9-linux-x86_64-threaded tcl-threaded
>>>
>>> cd ..
>>> }
>>>
>>> patch_namd () {
>>> cd colvars
>>> ./update-colvars-code.sh -f ../namd_cvs
>>> cd ..
>>> }
>>>
>>> compile_charm () {
>>> cd namd_cvs
>>>
>>> tar xf charm-*
>>> cd charm-*
>>> env MPICXX=mpicxx ./build charm++ mpi-linux-x86_64 --no-build-shared
>>> --with-production
>>>
>>> cd ../..
>>> }
>>>
>>> config_namd () {
>>> cd namd_cvs
>>> ./config Linux-x86_64-icc --charm-arch mpi-linux-x86_64
>>> cd ..
>>> }
>>>
>>> compile_namd () {
>>> cd namd_cvs
>>> cd Linux-x86_64-icc
>>>
>>> make depends
>>> make -j 4 release
>>>
>>> cd ../..
>>> }
>>>
>>> download_namd
>>> download_colvars
>>> download_fftw_tcl
>>>
>>> patch_namd
>>>
>>> compile_charm
>>>
>>> config_namd
>>> compile_namd
>>>
>>> #===================================================
>>>
>>>
>>> =========================================
>>> Reza Salari, M.D. Ph.D.
>>> Postdoctoral Researcher
>>> Center for Computational and Integrative Biology
>>> Rutgers University
>>> Science Building
>>> Camden, NJ 08102
>>> (856) 225-6492
>>> =========================================
>>>
>>
>
This archive was generated by hypermail 2.1.6 : Tue Dec 27 2016 - 23:22:08 CST