Dear all,
Can anybody tell me how to calculate the free energy difference after
running simulation with lamda(0, 0.1,...1)?
I am following the tutorial on wiki, but i have no idea about the
details to do the "data analysis".
any software can do it? and any reference for the instruction? I am ne
Dear all Gmxers,
I am calculating a mutation free energy from L<->A for a five AA
peptides using G96 53a6 force field.
however, my dG_for and dG_rev is quite different.
dG_for(lambda=0.00) = - 9.9 kJ/mol
dG_rev(lambda=1.00) = 1.33 kJ/mol
Is there anything wrong with setting up topologies?
H
Thanks for advice. I will test it.
Qiang
ggroenh wrote:
To rule out a sampling problem you can perform the simulations with
everything else frozen or position restraints. Both backwards and
forwards, and you can do it very fast, as there is nothing to
equilibrate. If there is still a discrepa
hi all,
I newly installed GROMACS on UBUNTU 7.10 from Synaptic Package
Manager(SPM). However, it can not pass the gamxtest with log as below,
but Tutorials seems OK.
Actually I try to compile myself at the beginning. It is weird that the
self-compiled one can pass the test but failed to run Tutor
S entirely so that I can reinstall
from fresh? Hope we can do it.
thank you very much.
Li Qiang
On Wed, 2007-11-07 at 16:16 +0800, Yang Ye wrote:
> Hi,
>
> You shall always try to build gromacs yourself. What's the error with
> tutorial?
>
> Regards,
> Yang Ye
>
version.
>
> Put that line "source ..." into ~/.bashrc shall make it default for
> every login session.
>
> Regards,
> Yang Ye
>
> On 11/7/2007 4:35 PM, Li Qiang wrote:
> > hi yang,
> >
> > thanks for the reply. Do you mean that the installation
confirm the problem.
thanks to all the information
Li Qiang
On Fri, 2007-11-09 at 00:11 +0800, Yang Ye wrote:
> got solved?
>
> I am using Ubuntu 6.10 after updating its packages, gromacs still fail
> on the simple/rb1 test, in a symptom similar to Li Qiang's.
> 3.3.1 is able t
I see. thanks for the information.
but one of my friends nearby failed on this combination just few hours
ago. Maybe we need more test for the conclusion.
Li Qiang
On Fri, 2007-11-09 at 10:47 +, Bruce Milne wrote:
> Dear Li Qiang,
>
> >> it seems another guy get the same er
Yes. Mine is 32-bit. Intel P4 3.0G.
On Fri, 2007-11-09 at 10:47 +, Bruce Milne wrote:
> Dear Li Qiang,
>
> >> it seems another guy get the same error(cannot pass gmxtest with
> >> rb1/acetonitrilRF) as me. and it sounds like the compatible problem
> >> bet
Dear Gromacs Users,
I wonder if it is normal for a protein to move out of the box during MD
runs. periodic boundary conditions are applied. system is neutralized.
0.9nm for the distance between box side and protein.
thanks
the md.mdp for your reference:
title = trp-Cage
cpp
Dear all users,
I want to plot the velocities of center of mass for my peptide. Reading
from 3.3 manual, there seems to be two ways--g_com and g_traj.
However,
1, g_com can not be found in /usr/local/gromacs/bin. Is there anything
missed for my installation?
2, $> g_traj -f md.trr -s md.tpr -o
Dear all,
I am simulating short peptide in GROMACS. Center of mass need to be
removed to keep the peptide from jumping out.
I have two questions about this:
1, when I remove COM of the peptide using comm_grps, do I need to put
the solvent(including the counter ion) at the same time for COM remov
) of COM is "constant".
Yes. the default way GROMACS do is system COM removal at each step.
how does the program remove this center of mass motion?
Merry Xmas
Qiang
On Wed, 2007-12-26 at 14:52 +0800, Christian Burisch wrote:
> Li Qiang schrieb:
> > Dear all,
>
&
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