On 2011-11-20 03:03, ÏéÇ« ¿× wrote:
Dear Mark,
Thanks for your prompt reply!
Pre-equilibration at the right temperature is always a good
idea, not just for REMD.
Right temperature? I guess you mean pre-equilibrate at every replica
temperatures, do you think so?
However for NVT REMD you need to
equilibrate the other temperatures at the same box size that
is sound for the temperature at which you want to make
observations.
If i am interested in the properties at 3OOK, i may equilibrate the system
at 300K with NPT ensemble, then equilibrate system at every replica
temperatures with the same box size obtained from the NPT simulation at 300K.Is
it right?
Why would you want to simulate at high pressure and high temperature?
Your proteins will unfold even faster. NVT REMD means your replicas
above 300 K will have too high P, at 360 K close to 1000 bar. Check
http://folding.bmc.uu.se/remd/index.php if you need to choose T for
REMD. The paper that describes the algorithm was published here:
http://dx.doi.org/10.1039/b716554d
Even given that, there is no strong reason to suppose that
a temperature distribution following a simple mathematical
formula should lead to equal exchange probabilities on a
"real" system with free energy bottlenecks. Knowing that one
might need to be adding more replicas at relevant
temperatures is something that can only be determined
empirically - and probably from more than 2ns.
Yes, that's right! While the exchange probabilities were unequal for
neighboring temperatures and maybe very high (0.3~0.4), i think i should remove
some replicas at which the exchange probabilities were higher and add some
replicas to increase the upper limit of the temperature range for REMD.
Meanwhile, anther question, what's the proper range for the exchange
probability? Does the high exchange probability impair the properties we want
to observe or just a waste of computational resources?
Best regards!
Xiangqian Kong
--- On Sat, 11/19/11, Mark Abraham<mark.abra...@anu.edu.au> wrote:
From: Mark Abraham<mark.abra...@anu.edu.au>
Subject: Re: [gmx-users] Poor exchange probability for REMD
To: "Discussion list for GROMACS users"<gmx-users@gromacs.org>
Date: Saturday, November 19, 2011, 12:14 AM
On 18/11/2011 12:43 PM, ÏéÇ« ¿×
wrote:
Dear GMX users，
Recently i am performing the
REMD simulation with Gromacs program and the temperature
distribution for each replica was predicted with the server
"http://folding.bmc.uu.se/remd/";. However, after a 2-ns
short test simulation with 64 replicas , i checked the
exchange probability for the neighboring replicas and find
the exchange probability was about 0.3 to 0.4 (as the file i
attached )but the desired probability was 0.2. Meanwhile, i
found the exchange probabilities fluctuated markedly for
each pair of replicas while ideally we may hope they
were consistent with each other. I don't know whether
this is acceptable or must be fixed up, or a longer
simulation time and pre-equilibrium at different replica
temperature for each replica was needed.
Pre-equilibration at the right temperature is always a good
idea, not just for REMD. However for NVT REMD you need to
equilibrate the other temperatures at the same box size that
is sound for the temperature at which you want to make
observations.
Even given that, there is no strong reason to suppose that
a temperature distribution following a simple mathematical
formula should lead to equal exchange probabilities on a
"real" system with free energy bottlenecks. Knowing that one
might need to be adding more replicas at relevant
temperatures is something that can only be determined
empirically - and probably from more than 2ns.
Mark
The system i simulated
includes 60074 atoms which consists of 155 residues,19173
waters and 14 chloridions. I first equilibrium the system
for 2ns with NPT ensemble at 300K, then start the REMD
simulation for 64 different replicas (temperature ranges
from 300 to 386K) with NVT ensemble and the exchange attempt
time was 2-ps(1000 integral steps).
Now i was totally puzzled and
don't know how to figure out these problems,i am eager for
the help from you and any suggestions will be greatly
appreciated!
Best regards!
Xiangqian Kong
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