From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Mar 26 2012 - 00:39:38 CDT
Just run your simulations and use the namdplot plugin in vmd to plot your temperature over time. So you will see if your energy conservation is ok.
Norman Geist.
Von: Molecular Dynamics [mailto:moleculardynamics_at_yahoo.com]
Gesendet: Freitag, 23. März 2012 15:18
An: Norman Geist
Betreff: Yan: AW: namd-l: conf file question
Dear Norman Geist,
Could you please give me some information about this issue ? What should I do also ?
Best regards.
_____
Kimden: Norman Geist <norman.geist_at_uni-greifswald.de>
Kime: 'Molecular Dynamics' <moleculardynamics_at_yahoo.com>
Kopya: Namd Mailing List <namd-l_at_ks.uiuc.edu>
Gönderildiği Tarih: 23 Mart 2012 13:09 Cuma
Konu: AW: namd-l: conf file question
Looks ok, but that‘s something you need to observe for system specially.
Norman Geist.
Von: Molecular Dynamics [mailto:moleculardynamics_at_yahoo.com]
Gesendet: Freitag, 23. März 2012 08:36
An: Norman Geist
Betreff: AW: namd-l: conf file question
Dear Norman Geist,
Thanks for your help. I think that I should choose fullElectFrequency 2 and this will be more suitable for my conf file. Could you please share your thougts about this issue ? Which value is suitable for my conf file ? By the way I don't run on GPUs. But I want to run my md simulations on GPUs in stead of CPUs. GPUs is nearly 5x faster than CPUs.
Best regards.
# Integrator Parameters
timestep 2 # 2 fs
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
rigidBonds all
_____
Kimden: Norman Geist <norman.geist_at_uni-greifswald.de>
Kime: 'Molecular Dynamics' <moleculardynamics_at_yahoo.com>
Gönderildiği Tarih: 23 Mart 2012 8:40 Cuma
Konu: AW: namd-l: conf file question
Hi,
looks ok for me, I think you got the points.
Please expect a bad energy conservation with fullelectfrequency 5. Are you running on GPUs?
Good luck
Norman Geist.
Von: Molecular Dynamics [mailto:moleculardynamics_at_yahoo.com]
Gesendet: Donnerstag, 22. März 2012 10:13
An: Norman Geist
Betreff: AW: namd-l: conf file question
Dear Norman Geist,
Thanks for your reply. According to your valuable explanations I arranged the conf file with the comments for a general namd restart job conf file. Could you please look over the attached namd.conf file and confirm if I did it right ? If I missed or did something wrong in namd.conf file please warn me. I should definitely learn this procedure right for my thesis study. So Your answer will clarify the general restart procedure and also all what I wanted to know.
Thanks for your help.
Best regards.
_____
Kimden: Norman Geist <norman.geist_at_uni-greifswald.de>
Kime: 'Molecular Dynamics' <moleculardynamics_at_yahoo.com>
Kopya: Namd Mailing List <namd-l_at_ks.uiuc.edu>
Gönderildiği Tarih: 21 Mart 2012 17:27 Çarşamba
Konu: AW: namd-l: conf file question
Hi anonymus,
It’s hard to point out your problem. If you want to run a 10ns simulation and want to have 1000 frames, you just need to save your dcd every 10ps. The firsttimestep parameter is optional and only causes the step number to run from there, but it will nevertheless do the amount of steps you ordered.
firsttimestep 500
run 1000
will result in last frame to be 1500
I think thats what you wanted to know, if not please explain more.
Norman Geist.
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Molecular Dynamics
Gesendet: Mittwoch, 21. März 2012 10:20
An: namd-l_at_ks.uiuc.edu
Betreff: namd-l: conf file question
Dear namd experts,
I want to perform 10 ns md simulation for 1000 record in NVT ensamble for analysis of the system. To do this I searched for restart files and examined lots of files which are different from each other. Then I generated a restart conf file that starts from the last step in namd.out file . But I’m confused about restart procedure. And I’m not sure if my restart conf file is true for 10 ns with 1000 record . So I need an expert help . Could you please look over the attached conf file and share your thoughts with me ?
Best regards.
WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 2512500
WRITING COORDINATES TO DCD FILE AT STEP 2512500
WRITING COORDINATES TO RESTART FILE AT STEP 2512500
FINISHED WRITING RESTART COORDINATES
The last position output (seq=2512500) takes 0.006 seconds, 869.734 MB of memory in use
WRITING VELOCITIES TO RESTART FILE AT STEP 2512500
FINISHED WRITING RESTART VELOCITIES
The last velocity output (seq=2512500) takes 0.004 seconds, 869.734 MB of memory in use
WRITING FORCES TO DCD FILE AT STEP 2512500
The last force output (seq=2512500) takes 0.001 seconds, 868.934 MB of memory in use
WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 2512500
CLOSING EXTENDED SYSTEM TRAJECTORY FILE
WRITING COORDINATES TO OUTPUT FILE AT STEP 2512500
CLOSING COORDINATE DCD FILE
The last position output (seq=-2) takes 0.087 seconds, 869.355 MB of memory in use
WRITING VELOCITIES TO OUTPUT FILE AT STEP 2512500
CLOSING FORCE DCD FILE
The last velocity output (seq=-2) takes 0.070 seconds, 868.676 MB of memory in use
====================================================
WallClock: 151413.078125 CPUTime: 151413.078125 Memory: 868.675781 MB
End of program
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