From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Jul 08 2014 - 12:14:10 CDT
> enabling GBSA
>
I already use GB SASA
try the impact of “twoawayx yes” and if that helps try additionally
> “twoawayy yes”
>
Could you please redirect me to the pertinent literature?
explicit water works much better anyway and the problem of exchange ratios
> can be overcome with the TIGER variant of REMD
>
Could you please redirect me to TIGER literature?
At any event, I already completed (on a longer peptide) a T-REMD (on a
BlueGene/Q) under either explicit TIP3 water or GB SASA. Forgetting about
ergodicity, which can not be achieved, starting from random, unfolded, I
got substantially the same modeling. Should TIGER save money ...
francesco pietra
On Tue, Jul 8, 2014 at 8:12 AM, Norman Geist <norman.geist_at_uni-greifswald.de
> wrote:
> You can raise the precision and work load for implicit solvent REMD by
> enabling GBSA and increased cutoff ;)
>
>
>
> But seriously you may want to try the impact of “twoawayx yes” and if that
> helps try additionally “twoawayy yes”.
>
>
>
> See also that explicit water works much better anyway and the problem of
> exchange ratios can be overcome with the TIGER variant of REMD.
>
>
>
> Norman Geist.
>
>
>
> *Von:* Francesco Pietra [mailto:chiendarret_at_gmail.com]
> *Gesendet:* Dienstag, 8. Juli 2014 07:42
> *An:* NAMD; Norman Geist
> *Betreff:* Fwd: namd-l: REMD on IBM iDataPlex DX360M3
>
>
>
> At CINECA it has been determined that my REMD, with a peptide of 19 aa
> under GB conditions, provided too less for the GPUs. In fact, under
> explicit water conditions, I could run REMD with also the GPUs. If
> anything, I expected more from the GPUs under these conditions: like with
> only CPUs, very many replicas are needed in order to have adequate exchange.
>
> fp
>
>
>
> ---------- Forwarded message ----------
> From: *Francesco Pietra* <chiendarret_at_gmail.com>
> Date: Thu, Jul 3, 2014 at 4:42 PM
> Subject: Re: namd-l: REMD on IBM iDataPlex DX360M3
> To: Norman Geist <norman.geist_at_uni-greifswald.de>
> Cc: Namd Mailing List <namd-l_at_ks.uiuc.edu>
>
> We also have namd 2.10 compiled on the IBM machine. Hopefully someone
> more expert than me in hardware/software, and particularly on that IBM
> machine, will intervene from our side.
>
> francesco
>
>
>
> On Thu, Jul 3, 2014 at 12:42 PM, Norman Geist <
> norman.geist_at_uni-greifswald.de> wrote:
>
> Forgot to mention that I’m working with an MPI based build of namd 2.10
> nightly build which have native REMD support and might be required.
>
>
>
> Norman Geist.
>
>
>
> *Von:* Francesco Pietra [mailto:chiendarret_at_gmail.com]
> *Gesendet:* Donnerstag, 3.
>
> Juli 2014 11:54
>
>
> *An:* Norman Geist
> *Cc:* Namd Mailing List
>
> *Betreff:* Re: namd-l: REMD on IBM iDataPlex DX360M3
>
>
>
> I have no recent records. When we tried some months ago, it seemed that
> the problem is probably trying to make
> sure that every replica has the same number of MPI tasks + GPUs. Probably
> the GPUs can not be shared between replicas. However, I am giving second
> hand information, probably as bad as any second hand information.
>
> We had no problem on running the same jobs on a BlueGene/Q, except a lot
> of CPUs required. I hoped to save money through the GPUs (which perform
> excellently on the same iDataPlex DX360M3 for both normal MD and
> accelerated MD)
>
>
>
> francesco pietra
>
>
>
> On Thu, Jul 3, 2014 at 11:28 AM, Norman Geist <
> norman.geist_at_uni-greifswald.de> wrote:
>
> What happens if you try?
>
>
>
> Norman Geist.
>
>
>
> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> Auftrag von *Francesco Pietra
> *Gesendet:* Donnerstag, 3. Juli 2014 08:15
> *An:* NAMD
> *Betreff:* namd-l: REMD on IBM iDataPlex DX360M3
>
>
>
> Hello:
>
> Any recent success in carrying out replica exchange molecular dynamics on
>
> IBM iDataPlex DX360M3 by also utilizing the GPUs?
>
> thanks
>
>
>
> francesco pietra
>
>
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