Hi Mark,
Your analyses are
quite reasonable. The low-temperature replicas are indeed doing much more work
than the high-temperature replicas. As you said, the lowest temperature replica
in the 24-replica should take an amount of time comparable to that of the
lowest in the 42-replica. So for
nergies 4 442 28.722 13.7
0.3
Rest 4 8426.029 4012.4
96.6
---
Total 4 8726.270 4155.4
100.0
Qiong
On 7/02/201
Dear all gmx-users,
I have recently been testing the REMD
simulations. I was running simulations on a supercomputer system based
on the AMD Opteron 12-core (2.1 GHz) processors. The Gromacs 4.5.3
version was used.
I have a system of 5172 atoms, of which 138
atoms belong to solute and the
the interaction energy
(E_inter = E_(1+2) - E_1 - E_2). They also used PME to deal with the long range
electrostatic interaction. The force field they used is charmm.
Any advice or comment are welcome!
Thank you very much in advance.
Qiong
On 10/03/2010 7:56 AM, Qiong Zhang wrote:
Hi dear Mark
ot be decomposed group-wise." Maybe a better way
to overcome this is using the formula:
E_interact=E_tot(1-2)-E_tot(1)-E_tot(2)
Do you agree with this?
I am highly appreciative for all your help!
Qiong
On 9/03/2010 9:32 PM, Qiong Zhang wrote:
Hi gmx users,
I found the big discrepancy b
?
Thank you very much!
Qiong
[gmx-users] Re:problem with interaction energy calculated byg_energy
Qiong Zhang
Tue, 09 Mar 2010 01:17:02 -0800
Hi dear Mark,
Please ignor my last mail replied to you. I made some mistake
you use
in such interaction energy calculations?
Thank you very much!
Qiong
--- On Tue, 3/9/10, Qiong Zhang
wrote:
From: Qiong Zhang
Subject: Re:problem with interaction energy calculated by g_energy
To: gmx-users@gromacs.org
Date: Tuesday, March 9, 2010, 4:27 PM
Hi dea
e excluded.
Am I right here?
For the second summing up problem, I am still checking all the input file,
especially the index file.
Thank you very much!
Qiong
- Original Message -
From: Qiong Zhang
Date: Monday, March 8, 2010 20:35
Subject: [gmx-users] problem with interaction energy ca
Dear gmx users,
I am studying the adsorption behavior of a molecule ( molecule 1) on a surface
(molecules 2). Based on the production run, I calculated the interaction energy
between molecule 1 and molecules 2 by g_energy.
Here comes the first question: Why only short range interactions between
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