Hi Matt,
On Jun 2, 2006, at 8:20 PM, [EMAIL PROTECTED] wrote:
From my browsing of list archives I can only recall seeing advice
that hyperthreading
cannot offer more Gromacs performance. For all I know this remains
true if you're trying
to use MPI to accelerate single calculations on
Oops... I've another new problem, that there wasn't before
---
Program mdrun_d, VERSION 3.3.1
Source code file: pullinit.c, line: 244
Fatal error:
Can not do constraint force calculation in parallel!
I certainly don't, but there are a couple of publications that
parametrize
heme for amber. You might want to see if those can be moved over (or if
you
can use the amber ports to gromacs) before digging in.
references:
J. Comput. Chem. 25:1613 (DFT on reduced and oxidized for cytochrome c)
J.
We have developed an accurate OPLS force field for P450 heme that includes O2 and thiolate ligands. The total charge is distributed among heme and ligands so this is not a force field for a standalone heme group. We did not deposit yet in contributions this force field but we can send you the
Dear all Gromacs users, Does anyone have an opinion about the following: Given a certain amount of time and computer power available, is it better in general to do short simulations for many lambda values or to do long simulations for fewer lambda values? Thanks for all the good advices on the
The first and last carbons are not calculated.
GROMACS needs to use a C-C bond on either side of each
carbon to place the hydrogens, and hence calculate the
order parameter.
--- Arneh Babakhani [EMAIL PROTECTED]
wrote:
Hello,
Now with the g_order bug fixed (see bugzilla #84) ,
I'm trying
Hi Alan, great, thanks, I suspected something like that.
Then, is there a way to calculate the Scd order parameters for these
carbons, given that there are no explicit hydrogens???
Arneh
Alan Dodd wrote:
The first and last carbons are not calculated.
GROMACS needs to use a C-C bond on
Well, for the terminal methyl, you have no way of
knowing which way the hydrogeons are pointing... So
no. However, it is worth including the carbonyl
carbon (although it has no hydrogeons, so no order
parameter), as a reference point for the next carbon
down.
--- Arneh Babakhani [EMAIL
Ok great, will do, thanks for your help!
Alan Dodd wrote:
Well, for the terminal methyl, you have no way of
knowing which way the hydrogeons are pointing... So
no. However, it is worth including the carbonyl
carbon (although it has no hydrogeons, so no order
parameter), as a reference point
Hi, GMXers,
i've some doubts about the use of GMX and implicit solvent models.
I have an huge system ( moreless 10 000 protein atoms) and trying to do MD
using explicit solvents but my computer limitations doesn't work very well.
1) someone could help me giving some light in how can i simulate
Hi David,First, thank you very much for your elaborate answer to my question.Your fast response has given me a little time to think about the infoyou supplied. Quoting David Mobley [EMAIL PROTECTED]: Soren, Given a certain amount of time and computer power available, is it better in general
Bharat, Matt, Tsjerk, and all,
I just put a bit of a tutorial on free energy calculations up at
http://www.dillgroup.ucsf.edu/~jchodera/group/wiki/index.php/Free_Energy:_Tutorial.
This will probably be a work in progress; it is not as step-by-step as
Tsjerk's (although possibly I could make it
Samuel Silva Pita wrote:
Hi, GMXers,
i've some doubts about the use of GMX and implicit solvent models.
I have an huge system ( moreless 10 000 protein atoms) and trying to do MD
using explicit solvents but my computer limitations doesn't work very well.
1) someone could help me giving some
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