Yes, I got exchanges. By construction! :-)
Email me off-list if you would like a methods description (for what it is
worth).
Mark
On Thu, Apr 25, 2013 at 1:11 PM, massimo sandal wrote:
> This hints at an interesting protocol/attempt, at least for a sort of
> newbie like me. Can you elaborate?
This hints at an interesting protocol/attempt, at least for a sort of
newbie like me. Can you elaborate? Did they exchange?
On 25 Apr 2013 13:06, "Mark Abraham" wrote:
> Likewise, I agreed with what Massimo said.
>
> As an example, I recently did a fairly large set of REMD simulations of a
> 320-
Likewise, I agreed with what Massimo said.
As an example, I recently did a fairly large set of REMD simulations of a
320-atom disordered peptide with rather more water and many fewer replicas
than you propose. I did so because I expected low barriers and large
maximum diameter (the latter from an
Don't be sorry. It's okay. It's just cultural differences.
2013/4/24 bharat gupta
> I think it should be me who should be sorry. I should have asked the
> question again in the forum without referring to some particular
> individual.
>
>
> On Wed, Apr 24, 2013 at 9:30 PM, massimo sandal >wrote
I think it should be me who should be sorry. I should have asked the
question again in the forum without referring to some particular
individual.
On Wed, Apr 24, 2013 at 9:30 PM, massimo sandal wrote:
> 2013/4/24 Justin Lemkul
>
> >
> >
> > I haven't said anything because I agree with what Mass
2013/4/24 Justin Lemkul
>
>
> I haven't said anything because I agree with what Massimo has already told
> you. If that is comforting in some way to know, then so be it, but I think
> it is rather rude to suggest that you would rather someone else answer your
> question, even after being given t
On 4/23/13 9:43 PM, bharat gupta wrote:
Dear Justin/Mark,
I have asked this question previously in the forum, I got some reply from
other members. It will be more useful if you can provide you expert
comments on the same. I am planning to run REMD for a peptide (406 atoms )+
solvent system (27
Dear Justin/Mark,
I have asked this question previously in the forum, I got some reply from
other members. It will be more useful if you can provide you expert
comments on the same. I am planning to run REMD for a peptide (406 atoms )+
solvent system (27639). The temperature range I selected is fr
In general, the smaller is your system, the less temperatures you will need
(and you'll have better performance).
Notice however that implicit solvent, while surely a possibility worth
considering, is not usually considered to be very good -take care that if
you write a paper from implicit solvent
Thanks a lot for your prompt responses. By using implicit solvent , I am
getting on 9 temperature values. I think this should work , I will try it
out. Also, i checked that when the no. of water molecules are reduced , the
no. of temp. values are also reduced. If I reduce the no. of water
molecules
In general, look in the literature what other people have done on similar
systems, and try to go from there.
2013/4/23 massimo sandal
> It depends on what you want to do. Possible it is certainly possible, but
> you can't be guaranteed to observe the conformational changes you desire to
> obser
It depends on what you want to do. Possible it is certainly possible, but
you can't be guaranteed to observe the conformational changes you desire to
observe. Again, it does not depend only on the REMD, but also on the length
of it. How long will it be? 10 ns? 100? 1000? 10.000? Plus, it also depen
So, my final question is whether is possible to do REMD for my system,
using the computational resource that I have.
On Tue, Apr 23, 2013 at 10:06 PM, massimo sandal wrote:
> Who knows? It depends on the size of your peptide, on the energy landscape,
> on how long is the run you plan to do. I wo
Who knows? It depends on the size of your peptide, on the energy landscape,
on how long is the run you plan to do. I would bet on "no", however.
2013/4/23 bharat gupta
> But if I choose a smaller temperature range , would it be possible to
> observe any folding event ??
>
>
> On Tue, Apr 23, 20
But if I choose a smaller temperature range , would it be possible to
observe any folding event ??
On Tue, Apr 23, 2013 at 9:16 PM, massimo sandal wrote:
> Thanks, now it's clearer.
>
> > Now, how can I temp. from these, so that the replicas can exchange ...
>
> You can't, I would say. The syste
Thanks, now it's clearer.
> Now, how can I temp. from these, so that the replicas can exchange ...
You can't, I would say. The system you have requires so many replicas to
exchange properly from the two temperature extremes you set up. As you have
seen, if you pick up temperatures in that range r
Sorry for that, I explain it again. Actually, I used the this link to
generate a temp. distribution. But I can do REMD for 56 replicas only, as I
have 56 processors available. The t-remd calculator provides 220
temperature values :
300.00, 301.01, 302.02, 303.04, 304.06, 305.08, 306.11, 307.14, 30
I don't understand your question. If you got the temperature distribution,
what else do you need?
2013/4/23 bharat gupta
> I have got the temperature distribution from the same link, but how to
> select evenly spaced temperatures for 56 replicas, I need to know that
>
>
> On Tue, Apr 23, 2013 a
I have got the temperature distribution from the same link, but how to
select evenly spaced temperatures for 56 replicas, I need to know that
On Tue, Apr 23, 2013 at 6:21 PM, massimo sandal wrote:
> Look here: http://folding.bmc.uu.se/remd/
>
>
>
> 2013/4/23 bharat gupta
>
> > Dear gmx users,
>
Look here: http://folding.bmc.uu.se/remd/
2013/4/23 bharat gupta
> Dear gmx users,
>
> I am planning to run REMD for a peptide (406 atoms )+ solvent system
> (27639). The temperature range I selected is from 300 to 500. I want to
> select appropriate temp. for 56 replicas. I randomly chose som
Dear gmx users,
I am planning to run REMD for a peptide (406 atoms )+ solvent system
(27639). The temperature range I selected is from 300 to 500. I want to
select appropriate temp. for 56 replicas. I randomly chose some temp
distribution and the exchange probabilities was 0.0. I know that we can
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