Hi,
I have done protein-drug simulations for 100ns. While calculating the hydrogen
bond between the protein-drug complex I am getting only 2 hydrogen bonds.
The number of H-bond formation is very low I have a question about is there
any influence of the drug in my protein?
With Regards,
*Saranya
Hi Justin
Thank you so much
with best
Farial
From: Justin Lemkul
To: gmx-us...@gromacs.org
Sent: Monday, 14 August 2017, 16:35:58
Subject: Re: [gmx-users] ligand
On 8/14/17 2:03 AM, farial tavakoli wrote:
> Dear Justin
> Thanks for your advice.Now I am
Dear GMX users
In order to benchmark my simulation system I would like to know in gromacs
which code scales linearly till 10K cores?
Thanks
Best Regards
Praveen
--
Thanks & Regards
Dr. Praveen Kumar Sappidi,
DST-National Postdoctoral Fellow
Computational Nanoscience Lab
Chemical Engineering
Whoever it was that did the coding for the cluster option, you did a
great job :-)
Been using it on some rather initially messy looking coordinate and
trajectory files in the last couple of weeks. Transforms them into
things of beauty.
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and
Hi all
I have a question on dealing with two reaction coordinates by gmx_wham. I
did umbrella sampling on glucose 6-phosphate molecule on a poly-Lys peptide
surface. Because the peptide is neither cylindrical nor spherical
symmetric, I have to restraint each window around a specific point, using
Dear All,
After a few tests, I finally got it.
Actually, the command line below does NOT generate a new set of group.
echo r 1-442 q|gmx make_ndx -f md_0_1.tpr -o index.ndx
Instead, it outputs ALL the 18 groups, each group contains its relevant atom
numbers.
After reading
Hi Mark,
Thank-you for the suggestion. Not sure if I’ve hit a bit of a circular problem.
Using Xcode clang and also a brew installed llvm I get this error during cmake:
-- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES) (found
version "1.0")
-- Could NOT find OpenMP_CXX
Hi Deepak,
I'd like to share a reference with you. http://www.tandfonline.
com/doi/abs/10.1080/00268970600893060
If you could take a look at results (14) versus (15), and results (28)
versus (29)... You see that when only the potential energy is considered,
the mass doesn't contribute to the
On 8/14/17 11:09 AM, ZHANG Cheng wrote:
Dear Gromacs,
After running
echo r 1-442 q|gmx make_ndx -f md_0_1.tpr -o index.ndx
I got a index.ndx file.
Then I run
echo 19 19|gmx rms -s md_0_1.tpr -f md_0_1.xtc -o rmsd.xvg -tu ns
But still only 18 options could be recognised. The index.ndx file is
Dear Gromacs,
After running
echo r 1-442 q|gmx make_ndx -f md_0_1.tpr -o index.ndx
I got a index.ndx file.
Then I run
echo 19 19|gmx rms -s md_0_1.tpr -f md_0_1.xtc -o rmsd.xvg -tu ns
But still only 18 options could be recognised. The index.ndx file is already in
the same folder.
So how to
Hi,
OK. That might be hard to work out how to fix, because I'm not sure we have
a Mac+AMD machine around. My guess is that somehow the compilation in the
driver assumes the use of xcode compilers, so that might be a thing for you
to try. The file it can't find is one that is installed as part of
Please don't reply to the entire digest, and be sure to change the
subject line.
On 8/14/17 9:51 AM, Faez Iqbal Khan wrote:
Dear Justin,
I talk to administrator
They said:
"Dear Faez,
I picked this up in your error file:
There is no domain decomposition for 105 ranks that is compatible
Hi Mark,
I've tried your suggestion. I've made an index file with my oxygen (O) and
my hydroxyl group (OH). Here my results:
H-bond average (calculated using num.xvg):
O = 1.10 +/- 0.62
OH = 2.06 +/- 0.66
(The first line from .log for each group)
# DonorHydrogen
Dear Justin,
I talk to administrator
They said:
"Dear Faez,
I picked this up in your error file:
There is no domain decomposition for 105 ranks that is compatible with the
given box and a minimum cell size of 1.025 nm
Change the number of ranks or mdrun option -rcon or -dds or your LINCS
blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px
#715FFA solid !important; padding-left:1ex !important; background-color:white
!important; } Dear justin
Thank you so much
Yours sincerelyFarial
Sent from Yahoo Mail for iPhone
On Monday, August 14, 2017, 4:35 PM,
Hi everyone,
I had some time on the weekend to try to troubleshoot this. Updating the BIOS
and trying different compilers didn’t help, but updating the kernel to 4.11.12
has made for a much more stable system. I ran a 1 ns five times and it only
crashed once.
Regards,
Steffen
> On Aug 8,
Hi Mark,
Here are the results for a few different runs:
(1) gmx mdrun -v -deffnm md_0_1 -nb cpu
Runs fine and completes
(2) gmx mdrun -v -deffnm md_0_1
Gives a similar error message:
---
Program: gmx mdrun, version 2016.2
Source file:
On 8/14/17 8:15 AM, ZHANG Cheng wrote:
Dear Gromacs,
My MD contains a protein (442 residues) and 203 free glycines. The numbering of
the residues is:
1-442: the protein residues
443-645: the 203 free glycines
When I use the "rms" command, all the 645 residues are considered as the
Hi,
I don't think so, because it's trivial - it's defined as the value of the
potential at the distance of the cutoff.
Mark
On Thu, 10 Aug 2017 19:44 Natalie Paige Schieber <
natalie.schie...@colorado.edu> wrote:
> Hi all,
>
> I am using the potential-shift-verlet keyword for the
Hi,
I would use the selection groups judiciously, for example have one of them
with only donor atoms in it.
Mark
On Fri, 11 Aug 2017 00:05 Marcelo Depólo wrote:
> Hi all!
>
>
> I've been wondering how donors and acceptors are defined in gmx hbond. In
> the help
Hi,
That's a bit mysterious, because we check that that works in our automated
testing. If running a simulation works then everything is fine, but it's
possible the same error arises. Can you try that, please, and report back?
Mark
On Fri, 11 Aug 2017 23:48 Steffen Graether
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
had useful information
Mark
On Mon, 14 Aug 2017 09:17 Neha Gupta wrote:
> Hi gromacs users,
>
> After simulation for 5 ns, I generated a movie.pdb file using .gro and .xtc
>
> However, in the
On 8/14/17 2:03 AM, farial tavakoli wrote:
Dear Justin
Thanks for your advice.Now I am trying to create a .gro file from the united
atom pdb structure file obtained from ATB by using :editconf -f xxx.pdb -o
xxx.gro
but faced to this warning:
WARNING: all CONECT records are ignored
would
Dear GROMACS Community,
I am trying to do a simulation using a tabulated potential which forces
me to use the group cut-off. I get a drift in the conserved quantity of
-600KJ/mol/ns. My system consists of 1000 rigid TIP4P water molecules
and a Na+ ion. It seems that the problem is in the group
On 14/08/17 09:17, Neha Gupta wrote:
Hi gromacs users,
After simulation for 5 ns, I generated a movie.pdb file using .gro and .xtc
However, in the movie file, I witnessed bizarre long bonds...
How to fix it?
Any suggestions please?
trjconv -pbc whole
Thanks,
Neha
--
David van der
Hi gromacs users,
After simulation for 5 ns, I generated a movie.pdb file using .gro and .xtc
However, in the movie file, I witnessed bizarre long bonds...
How to fix it?
Any suggestions please?
Thanks,
Neha
--
Gromacs Users mailing list
* Please search the archive at
Dear Justin
Thanks for your advice.Now I am trying to create a .gro file from the united
atom pdb structure file obtained from ATB by using :editconf -f xxx.pdb -o
xxx.gro
but faced to this warning:
WARNING: all CONECT records are ignored
would you please advice me how can i solve this problem?
27 matches
Mail list logo