if (bDoVdW_i || bDoCoul_i_sol)
1031c1046
< else if (!bDoCoul_i)
---
else if (!bDoCoul_i_sol)
Date: Mon, 2 Feb 2009 18:11:16 -0500
From: chris.ne...@utoronto.ca
To: gmx-users@gromacs.org
Subject: [gmx-users] free ener
Coul_i_sol)
> Date: Mon, 2 Feb 2009 18:11:16 -0500
> From: chris.ne...@utoronto.ca
> To: gmx-users@gromacs.org
> Subject: [gmx-users] free energy with TIP4P bug fixed
>
> Hi Berk,
>
> Could you please post the relevant cvs diff here? While my energies are now
> output
Hi Berk,
Could you please post the relevant cvs diff here? While my energies are now output consistently for zero-step mdruns while separating
my energygrps, I am still seeing some very aberrant behaviour when I apply the free-energy code during a 2-10 ns MD run,
even with lambda=0.0. I get the
Hi,
Sorry for not being clear on this issue.
I am currently following and preparing lectures and exercises for a workshop
and do not have time to sit back and go deeply into this issue.
What my conclusion is from looking at the code:
With TIP4P water and free-energy any non-perturbed atoms
that
Since I also use the pull code on these systems (while not using the
free energy code), I tested that system and verified that, for my
system, the tip4p-based Coulomb (SR) discrepancy does not appear to
result when the pull code is used in gromacs 4.0.3.
With pull code and using energygrps
I just realized that my previous post was incorrect on its final test.
The correct conclusion is:
I have done some tests that, for a single system, empirically indicate
that the coulomb(SR) discrepancy occurs only with use of the free
energy code and only when tip4p is in the same energygrps as
I have done some tests that, for a single system, empirically indicate
that the coulomb(SR) discrepancy occurs only with use of the free
energy code and only when tip4p is in the same energygrps as any part
of the molecule which is perturbed, even if the common atoms are not
perturbed thems
Yes, I could use clarification here as well.
I had previously suspected a specific bug relating to the free energy
code and water models (TIP4P-Ew) and contacted the list about this a
few weeks ago. At that time Berk told me that there was no
water-specific free energy code, which I take to mean t
Berk, David, and other developers,
I believe that all the relevant information has already been posted,
but since I use TIP4P ubiquitously, I would like to get some
clarification regarding simulations that may be affected. I currently
understand that:
1. Utilization of TIP4P in the absenc
Hi,
The Coulomb energy difference that Chris Neale observed recently
was caused by a bug in the neighborlist assignment with the combination
of free energy and tip4p water optimization.
This bug would cause a few tip4p-tip4p charge interactions to be missing.
I think it has been present in all Gr
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