Thank you Justing...
We are working on your observations...
We are sure that we will get back on this issue as soon as we figure out what
we have done wrong...
Best,
On Mon, 06 Aug 2012 15:29:04 -0400, Justin Lemkul wrote
> On 8/6/12 3:13 PM, Ramon Garduno wrote:
> > On Mon, 06 Aug 2012 13:52:4
On 8/6/12 3:13 PM, Ramon Garduno wrote:
On Mon, 06 Aug 2012 13:52:46 -0400, Justin Lemkul wrote
Please provide all the necessary files, including topologies and
modified force field files. I don't have time to make and double-
check all of these files and it's better to use exactly the same
On Mon, 06 Aug 2012 13:52:46 -0400, Justin Lemkul wrote
> Please provide all the necessary files, including topologies and
> modified force field files. I don't have time to make and double-
> check all of these files and it's better to use exactly the same
> files you've been trying to use.
>
On 8/6/12 1:35 PM, Ramon Garduno wrote:
Justin,
Of course you are right, for troubleshooting the smaller, the better. However,
in order to build a hydroxyapaptite (HAP) slab we need the proper unit cell,
the later is by no means small.
In response to your comments, I will appreciate very much
Justin,
Of course you are right, for troubleshooting the smaller, the better. However,
in order to build a hydroxyapaptite (HAP) slab we need the proper unit cell,
the later is by no means small.
In response to your comments, I will appreciate very much if you could examine
the PDB files related
On 7/27/12 8:54 PM, Ramon Garduno wrote:
Dear Justin,
Thanks for your quick reply. Actually, we think that the topology is OK,
however HAP's parameters could be wrong, we are checking on this...
I would say that the topology being OK and the parameters being wrong are
contradictory stateme
Dear Justin,
Thanks for your quick reply. Actually, we think that the topology is OK,
however HAP's parameters could be wrong, we are checking on this...
These are the topology files used for HAP. The names associated to the atoms
present on the slab are:
ACa - Ca2+
AP - P
AO1 - O(P)
AO4 - O(
On 7/25/12 2:32 PM, Ramon Garduno wrote:
Dear gmx friends:
We are modeling a solvated hydroxyapatite(HAP)-protein complex. We have
minimized and equilibrated this system to 300K under NVT.
The odd behavior is observed when we start an NPT simulation. In the very
first ps we observed that the
Dear gmx friends:
We are modeling a solvated hydroxyapatite(HAP)-protein complex. We have
minimized and equilibrated this system to 300K under NVT.
The odd behavior is observed when we start an NPT simulation. In the very
first ps we observed that the oxygens bound (initially) to phosphorous in
p
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