Dear gmx users
Could you please help me to create pdo files?I have finished my
umbrella sampling with position but g_wham wants pdo files but I can
not find any option to have these files after my run or create them.I
dont know what to do.Thanks a lot
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Cheers pal! :)
Steven
On Sat, Feb 18, 2012 at 9:42 AM, Jianguo Li wrote:
> One way to get the free energy is to measure the force as a function of
> distance and do the integration to get the PMF, as used in the paper:
> Ronen Zangi, Morten Hagen, and B. J. Berne. 2007. Effect of Ions on the
>
Hi,
If you have time, I have a question about the -xy option in g_rdf. I'm a
little afraid that this may be silly question and the answer might be
obvious in hindsight, but I have been having difficulty finding the answer.
Thanks.
As we all know, g_rdf computes radial distribution functions of,
Sorry I meant he default rcoulomb-switch is 0. I am using OPLSAA. Just
confused 0.1 nm switch distance to rc=1.1 doesnt give artifact. I think i
am confusing this with the buffer zone needed between rc and rlist!
On 18 February 2012 10:21, Mark Abraham wrote:
> On 19/02/2012 2:01 AM, Juliette
On 19/02/2012 2:01 AM, Juliette N. wrote:
Hi,
I am trying to figure out the best setting for cut offs and r_switch
for my system based on shift functions.
coulombtype = Shift
vdw-type= Shift
rcoulomb-switch = 1
rvdw-switch = 1
; Cut-offs
Hi,
I am trying to figure out the best setting for cut offs and r_switch for my
system based on shift functions.
coulombtype = Shift
vdw-type= Shift
rcoulomb-switch = 1
rvdw-switch = 1
; Cut-offs
rlist = 1.35
rcoulomb
dina dusti wrote:
Dear Gromacs Specialists,
Sometimes, when I do "g_analyze -f .xvg -av -ee error.xvg" , I take
following warning, and I don't know how to fix it.
Set 1: err.est. 0.000596502 a 0.29217 tau1 24.8856 tau2 443.641
Warning: tau2 is longer than the length of the data (
shahid nayeem wrote:
Dear All
I am doing umbrella sampling for a protein complex. After analysis I am
finding that prifle.xvg has not converged. Now I want to extend
simulation. I have already pulled one chain to the length of the box.
Can I further pull by extending the box size and add mo
On 18/02/2012 7:50 PM, xiaojiong wrote:
Dear,
My receptor is membrane proteins,then I get protein-ligand complex.I
want to do MD simulations in DPPC.I use the GROMOS96 53a6 force
field modified in order to include Berger’s parameters for lipids .The
topology for the ligand was created
employin
On 18/02/2012 7:23 PM, Banafsheh Mehrazma wrote:
Dear all;
I am wondering if the amber99 in gromacs package is the same as PARM99
in Amber package, so that I can use the new modified parameters (which
is made in Amber package) in my simulation in gromacs? Or should I
make some changes?
These sh
Dear Gromacs Specialists,
Sometimes, when I do "g_analyze -f .xvg -av -ee error.xvg" , I take
following warning, and I don't know how to fix it.
Set 1: err.est. 0.000596502 a 0.29217 tau1 24.8856 tau2 443.641
Warning: tau2 is longer than the length of the data (864000)
the st
One way to get the free energy is to measure the force as a function of
distance and do the integration to get the PMF, as used in the paper:
Ronen Zangi, Morten Hagen, and B. J. Berne. 2007. Effect of Ions on the
Hydrophobic Interaction betweenTwo Plates. J. AM. CHEM. SOC. 2007, 129,
4678-468
Dear Gmx Users,
I am wondering whether you know a technique for calculating the free energy
between charged surfaces - I want to calculate distance when the deltaG=0
so that the surfaces are in equilibrium - closer distance will make that
they repeal each other, longer (deltaG<0). Will Umbrella Sa
Dear,
My receptor is membrane proteins,then I get protein-ligand complex.I want to
do MD simulations in DPPC.I use the GROMOS96 53a6 force
field modified in order to include Berger’s parameters for lipids .The
topology for the ligand was created
employing the server PRODRG 2.5 Beta.
When I f
Dear all;
I am wondering if the amber99 in gromacs package is the same as PARM99
in Amber package, so that I can use the new modified parameters (which
is made in Amber package) in my simulation in gromacs? Or should I
make some changes?
Best regards;
Banafsheh
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