From: Horia Jalily Hasani (jalilyha_at_ualberta.ca)
Date: Tue Sep 13 2016 - 10:34:22 CDT
Thank you, Norman.
On Tue, Sep 13, 2016 at 12:19 AM, Norman Geist <
norman.geist_at_uni-greifswald.de> wrote:
> Although you could easily adapt the replica.namd script to produce entries
> in the history file more frequently, I doubt it makes sense. Since you said
> your system requires 50ps between swap attempts, more frequently generated
> frames will contain the same state over and over, so what would be the
> benefit?
>
>
>
> To have more frequent history writes, you would need to replace the single
> “run” command by series of run commands and generate the history entries
> in-between. But I don’t recommend doing that changes, since it doesn’t make
> sense to me at all and if you break the frame/history mapping while doing
> the changes, you might have wrong sorting later.
>
>
>
> I’d say if your system is that large, that it requires 50ps per swap as
> you said, then REMD might not be a suitable method for whatever you try to
> find out with it.
>
>
>
> Good luck
>
>
>
> Norman Geist
>
>
>
> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> Auftrag von *Horia Jalily Hasani
> *Gesendet:* Montag, 12. September 2016 18:22
> *An:* Norman Geist <norman.geist_at_uni-greifswald.de>
> *Cc:* <namd-l_at_ks.uiuc.edu> <namd-l_at_ks.uiuc.edu>
>
> *Betreff:* Re: namd-l: REMD and sortreplicas program
>
>
>
> Hi Norman,
>
>
>
> I have changed the dcd frequency in the replica namd script to be written
> every 1000 steps instead of steps_per_run*runs_per_frame (which would
> have been 50,000 in my case). I did this to obtain a wider sampling.
>
>
>
> The steps_per_run parameter is set to 50 ps because I have a huge system
> and I expect it to require these many steps to equilibrate before a swap.
>
>
>
> Now again for the replica namd script, do you think there is a way to
> increase the outputs in the history file with the current parameters? So,
> I would eventually obtain more frames in the sorted dcd file.
>
>
>
> dcdFreq 1000
>
> steps_per_run 50000
>
> set runs_per_frame 1
>
> set frames_per_restart 1
>
>
>
> Thanks,
>
> Horia
>
>
>
> On Mon, Sep 12, 2016 at 12:38 AM, Norman Geist <
> norman.geist_at_uni-greifswald.de> wrote:
>
> I meant steps_per_run*runs_per_frame
>
>
>
> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> Auftrag von *Norman Geist
> *Gesendet:* Montag, 12. September 2016 08:06
> *An:* 'Horia Jalily Hasani' <jalilyha_at_ualberta.ca>
> *Cc:* namd-l_at_ks.uiuc.edu
> *Betreff:* AW: namd-l: REMD and sortreplicas program
>
>
>
> Ok, it seems you are doing things very unusual O_o
>
> Usually the replica namd scripts set the dcdfreq to
> steps_per_run*frames_per_restart. So generally with reasonable input
> values, the history file has more entries than the dcd has frames ;)
>
>
>
> There are only some parameters that control how output is generated:
>
>
>
> 1. steps_per_run -> Number of timesteps between exchange attempts,
> usually between 2 and 5 picoseconds.
>
> 2. runs_per_frame -> Number of exchange attempts before writing a
> frame to the dcd, usually about 5
>
> 3. frames_per_restart -> Number of frames generated, before writing
> a set of restart files to continue, usually about 100
>
>
>
> So there’s no need to change replica.namd, just your input. Btw. why the
> hell did you choose 50ps as exchange frequence??
>
>
>
> Norman Geist
>
>
>
> *Von:* Horia Jalily Hasani [mailto:jalilyha_at_ualberta.ca
> <jalilyha_at_ualberta.ca>]
> *Gesendet:* Freitag, 9. September 2016 17:48
> *An:* Norman Geist <norman.geist_at_uni-greifswald.de>
> *Betreff:* Re: namd-l: REMD and sortreplicas program
>
>
>
> Also, I use:
>
> sortreplicas <job_output_root> <num_replicas> <runs_per_frame>
>
> in my case:
>
> sortreplicas <job_output_root> 128 1
>
>
>
>
>
> On Thu, Sep 8, 2016 at 11:22 AM, Horia Jalily Hasani <jalilyha_at_ualberta.ca>
> wrote:
>
> Hi Norman,
>
>
>
> Thanks for your reply.
>
> Yes, it's normal parallel tempering.
>
> I currently do an exchange after 50,000 steps, and so I get an entry in
> the history file only every 50,000 steps. Based on what you mentioned, this
> could explain the reason for sortreplicas giving me lesser frames in the
> sorted dcd files. I have only 50 entries and so I get only 50 frames in the
> sort.dcd file, whereas the initial dcd file has 2000 frames.
>
>
>
> So I will need to increase the entries in the history file to for example
> every 1000 steps instead of doing it based on steps_per_run parameter. And
> for that I suppose I will need to modify this section of the replica.namd
> file:
>
>
>
> while {$i_run < $num_runs} {
>
>
>
> run $steps_per_run
>
> save_array
>
> incr i_step $steps_per_run
>
> set TEMP $saved_array(TEMP)
>
> set POTENTIAL [expr $saved_array(TOTAL) - $saved_array(KINETIC)]
>
> puts $history_file "$i_step $replica(index) $NEWTEMP $TEMP $POTENTIAL"
>
>
>
> if { $i_run % 2 == 0 } {
>
> set swap a; set other b
>
> } else {
>
> set swap b; set other a
>
> }
>
>
>
>
>
> Please advise if I am on the right track and what would be the best way to
> edit it.
>
>
>
> Thanks,
>
> Horia
>
>
>
>
>
>
>
>
>
> On Thu, Sep 8, 2016 at 12:41 AM, Norman Geist <
> norman.geist_at_uni-greifswald.de> wrote:
>
> What kind of REMD did you perform? Just normal parallel tempering? If so,
> you should get all the frames in the sorted dcds for which you also have
> the corresponding history entry. Also, how did you call sortreplicas?
>
>
>
> Norman Geist
>
>
>
> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> Auftrag von *Horia Jalily Hasani
> *Gesendet:* Donnerstag, 8. September 2016 02:11
> *An:* <namd-l_at_ks.uiuc.edu> <namd-l_at_ks.uiuc.edu>
> *Betreff:* namd-l: REMD and sortreplicas program
>
>
>
> Hi,
>
>
>
> I have been performing REMD and I wonder if someone could give me a hint
> in the analysis part. When it comes to using the sortreplicas for sorting
> the dcd files and history files based on temperature, the program seems to
> take "only frames with the biasing potential V (d, i)" (quoted from
> the One-dimensional REUS tutorial).
>
>
>
> For example, if I give it trajectories each of which have 2000 frames, I
> end up getting only 50 frames in the sorted dcd files. But I am interested
> in having all the 2000 frames sorted based on temperature without
> considering the potential at that point.
>
>
>
> I would appreciate if anyone could give me a hint related to
> the sortreplicas program and if there is an alternative way of sorting the
> outputs based on temperature.
>
>
>
> Thanks,
>
> Horia
>
>
>
>
>
>
>
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