If you position restraint the receptor or only use several residues at the
binding site, in both cases you limit your sampling to a small part of the
phase space and the PMF may not be accurate, since the receptor may undergo
conformational change upon ligand binding.
Cheers
--Jianguo
-
Hello all,
Is there any way to calculate fraction of native contacts during the
simulation in gromacs. I searched the archives but didn't found any
significant clue.
*--
---
Thanks and Regards,
Bipin Singh*
--
gmx-users mailing listgmx-users@gromacs.org
On 10/30/12 4:23 PM, mtso wrote:
When trying to do an npt run, I get the fatal error: The X-size of the box
(3.999511) times the triclinic skew factor (1.00) is smaller than the
number of DD cells (4) times the smallest allowed cell size (1.00). I
should mention, I'm brand new to
On 10/31/12 4:10 AM, Nur Syafiqah Abdul Ghani wrote:
Dear All,
Currently I'm doing the minimization part for my solvent which is
hexafluoroisopropanol with water.
I'm packing them with packmol then use the forcefield gromos96.
Now by using the command
grompp -f em1.mdp -c minimize_301012.gro
On 10/31/12 6:02 AM, bipin singh wrote:
Hello all,
Is there any way to calculate fraction of native contacts during the
simulation in gromacs. I searched the archives but didn't found any
significant clue.
At present, there is no way to do this. Likely one could modify the g_mindist
code
Technically, in order to show that your simulation has reached complete
convergence, you would need to
show that every type of data has converged. Obviously nobody does this. You
should start with looking at the
convergence of any data type that you analyze in any other way. i.e. if you
show a
Thanks Justin,
We're using the tutorial, and those .mdp files as a starting point but
actually running the simulations on the protein PDB ID 2LFM, without adding
a ligand for now, and modifying the .mdp files as necessary.
--
View this message in context:
On 10/31/12 10:23 AM, mtso wrote:
Thanks Justin,
We're using the tutorial, and those .mdp files as a starting point but
actually running the simulations on the protein PDB ID 2LFM, without adding
a ligand for now, and modifying the .mdp files as necessary.
Just make sure whatever changes
Hi all,
I wanted to test the built-in support in Gromacs 4.6 (non-OpenMM) for GPUs.
I downloaded the latest git version and it built successfully, appears
to link the right CUDA libraries etc.
I tried testing it with the Gromacs GPU benchmark suite
Dear Ali:
I am not sure what ecenter is, it looks like it might be the position to which
the user wants to set the center?
In any event, it doesn't mater for this modification.
I did not write the center_x() function, it is a standard part of gmx_trjconv.c
What I did was to copy center_x() to
Leila, I provided 2 good references to answer your question earlier. If you
can't be bothered to read about it,
then the answer is yes, it is a good method.
Looking at your other questions, I think that it is time for you to look at
those references and learn more about
block averaging and
Dear Justin Thank you For your Previous Kind Reply
I
am following your Lipid-protein Tutorial for My system I Gave The Following
Commands As Quoted in your Tutorial Also I Have Suitably Edited The Topology As
On 10/31/12 11:45 AM, vidhya sankar wrote:
Dear Justin Thank you For your Previous Kind Reply
I am following your Lipid-protein Tutorial for My system I Gave The
Following Commands As Quoted in your Tutorial
Hi,
you can use the tpr files from the tgz if you use the non-implicit solv
(preferable PME) test.
Roland
On Wed, Oct 31, 2012 at 10:37 AM, Susan Chacko sus...@helix.nih.gov wrote:
Hi all,
I wanted to test the built-in support in Gromacs 4.6 (non-OpenMM) for GPUs.
I downloaded the latest
Thank you! Yes, I am able to run the 'dhfr-solv-PME.bench' benchmark with
mdrun -s topol.tpr -testverlet
and it seems to be using the GPUs as well:
---
2 GPUs detected:
#0: NVIDIA Tesla M2050, compute cap.: 2.0, ECC: yes, stat: compatible
#1: NVIDIA Tesla M2050, compute cap.: 2.0, ECC: yes,
Just make sure whatever changes you are making are correct for the chosen
force
field and algorithms. If you're having problems with NPT, you can always
switch
to the Berendsen algorithm for pressure coupling before returning to
Parrinello-Rahman for data collection.
-Justin
Thanks for the
On 10/31/12 12:38 PM, mtso wrote:
Just make sure whatever changes you are making are correct for the chosen
force
field and algorithms. If you're having problems with NPT, you can always
switch
to the Berendsen algorithm for pressure coupling before returning to
Parrinello-Rahman for
I've asked the same question myself and would also like to know.
That said, there seems to be no issue if you set refcoord_scaling=com.
According to the manual, this does
not give artefacts (whatever they are) and also does not change your restraint
positions (as refcoord_scaling=all
does).
As I understand it, position restraints for an atom are set in the topology
file and applied to that atom in each of that species. In order to restrain
some but not all of the water I'd have to copy the topology of my water
model and add the restraints, then rename (and group together) the atoms I
No need to rename... just make an .ndx group.
-- original message --
As I understand it, position restraints for an atom are set in the topology
file and applied to that atom in each of that species. In order to restrain
some but not all of the water I'd have to copy the topology of my water
Chris, is that for freeze groups or position restraints?
On Wed, Oct 31, 2012 at 3:22 PM, Christopher Neale
chris.ne...@mail.utoronto.ca wrote:
No need to rename... just make an .ndx group.
-- original message --
As I understand it, position restraints for an atom are set in the topology
On 10/31/12 3:55 PM, Alex Marshall wrote:
Chris, is that for freeze groups or position restraints?
I will assume Chris was referring to the restraint method - you need an index
file for creating the position restraint .itp file using genrestr. It will save
you a ton of time over doing it
Well, I thought that it would work for for freeze groups, and that is what I
intended to say. I've used freeze groups
before, but don't have tonnes of experience with them. The gromacs mdp options
page reads as if it should work (
http://manual.gromacs.org/online/mdp_opt.html#neq ), but if
On 10/31/12 4:21 PM, Christopher Neale wrote:
Well, I thought that it would work for for freeze groups, and that is what I
intended to say. I've used freeze groups
before, but don't have tonnes of experience with them. The gromacs mdp options
page reads as if it should work (
makes sense.
-- original message --
On 10/31/12 4:21 PM, Christopher Neale wrote:
Well, I thought that it would work for for freeze groups, and that is what I
intended to say. I've used freeze groups
before, but don't have tonnes of experience with them. The gromacs mdp
options page reads
On 10/31/12 4:56 PM, Ali Alizadeh wrote:
Dear All users
I have a system that contains water , methane and propane in 240 k and 300
bar,
My simulation box is rectangular .
Water film is in middle of my box. Methane and propane is around it.
My simulation box is symmetric,
1- I used g_rdf
Dear Ali:
I don't think that you are re-posting the same question often enough.
Perhaps you should repost more often? 4 identical posts in 5 hours might not be
enough to get a reply
Seriously though, we all saw your message.
Chris.
-- original message(s) --
I have a system that
hi Gmxers,
is the Hessian matrix unit in gmx is ps^(-2), or
J *mol^(-1) nm^(-2)?
thanks,
Yao
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* Please search the archive at
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Thank you so much!
-原始邮件-
发件人: Jianguo Li ljg...@yahoo.com.sg
发送时间: 2012年10月31日 星期三
收件人: Discussion list for GROMACS users gmx-users@gromacs.org
抄送:
主题: Re: [gmx-users] steered pulling code on ligand-receptor complex
If you position restraint the receptor or only use several
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