Hi,
Use a visualization program and see what you learn...
Mark
On Mon, Aug 25, 2014 at 8:26 AM, Lovika Moudgil
wrote:
> I am trying to have a system of GNPs with aminoacid and stabilizer i.e
> Sodium Citrate ...and this hydrogen is of Sodium Citrate . moving
> molecule is not working f
I am trying to have a system of GNPs with aminoacid and stabilizer i.e
Sodium Citrate ...and this hydrogen is of Sodium Citrate . moving
molecule is not working for me!!!
Regards
Lovika
On Mon, Aug 25, 2014 at 10:52 AM, Kester Wong wrote:
> If the H-atom is constituent of a molecule (e.
thank you very much sir.
regards
Suriyanarayanan
On Sat, Aug 23, 2014 at 12:06 AM, Tsjerk Wassenaar
wrote:
> Hi Suriyanarayanan,
>
> You can check out the WeNMR Gromacs portal.
>
> Hope it helps,
>
> Tsjerk
> On Aug 22, 2014 10:29 AM, "Balasubramanian Suriyanarayanan" <
> bsns...@gmail.com> wr
You could ask for it to be installed?
Mark
On Mon, Aug 25, 2014 at 2:01 AM, Nikolaos Michelarakis
wrote:
> Hello,
>
> I am trying to do a secondary structure analysis to get the percentages of
> each secondary structure in my protein. I know i can use do_dssp but
> unfortunately DSSP is not in
Hi,
How about using the Gromacs/tools package provided at that site? It seems
to bundle all the tools, and presumably its build system works (and if it
doesn't, please enquire first of the authors of modified versions, since
they're the ones able to fix any problems).
Mark
On Mon, Aug 25, 2014
On Mon, Aug 25, 2014 at 5:01 AM, Theodore Si wrote:
> Hi,
>
> https://onedrive.live.com/redir?resid=990FCE59E48164A4!
> 2572&authkey=!AP82sTNxS6MHgUk&ithint=file%2clog
> https://onedrive.live.com/redir?resid=990FCE59E48164A4!
> 2482&authkey=!APLkizOBzXtPHxs&ithint=file%2clog
>
> These are 2 log f
use -missing in last of command pdb2gmx
On Mon, Aug 25, 2014 at 10:54 AM, neha bharti wrote:
> Hello All
>
> I am performing Molecular dynamics simulation of protein-ligand complex
> using charmm36 force field in popc lipid.
>
> I downloaded the protein ligand complex pdb file. And as mentioned i
If the H-atom is constituent of a molecule (e.g. H2O), then you could also try moving the molecule coordinates and see how it goes.I had a similar issue, but moving the molecule by an angstrom worked in my case. Good luck!Regards,Kester- 원본 메일 -보낸사람 : Lovika Moudgil 받는사람 : 받은날짜 : 2
Hello All
I am performing Molecular dynamics simulation of protein-ligand complex
using charmm36 force field in popc lipid.
I downloaded the protein ligand complex pdb file. And as mentioned in
Justin A. Lemkul protein-ligand complex tutorial I have seperate ligand and
protein from pdb file.
My
Dear Justin
In /home/atila/gromacs-4.0.4/src/tools, when I use gcc g_vesicle_density.c
I encountered with
g_vesicle_density.c:26:21: error: gmx_ana.h: No such file or directory
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_
Please upload them to a file-sharing service on the web (there are lots
that are free-to-use), and paste the link here.
Mark
On Mon, Aug 25, 2014 at 6:07 AM, Yunlong Liu wrote:
> Hi Szilard,
>
> I would like to send you the log file and i really need your help. Please
> trust me that i have te
So, that means either your starting configuration or your model physics
doesn't make sense. Which is it?
Mark
On Mon, Aug 25, 2014 at 6:52 AM, Lovika Moudgil
wrote:
> Thanks for reply Justin and Kester...Ya my geometry is getting distorted
> and I tried to change the coordinates of atom 19 i.e
Dear Justin
Thanks for your answer.
Unfortunately, I am not professional in Linux OS. This project is important
for me.
Please guide me to do that truly.
How to compile these c files?
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GM
Thanks for reply Justin and Kester...Ya my geometry is getting distorted
and I tried to change the coordinates of atom 19 i.e Hydrogen ...but the
error is same
Regards
Lovika
On Mon, Aug 25, 2014 at 7:09 AM, Kester Wong wrote:
> Dear Lovika,
>
>
> Have you looked into atom 19 specifically
Hi Szilard,
I would like to send you the log file and i really need your help. Please trust
me that i have tested many times when i turned on the dlb, the gpu nodes
reported cannot allocate memory error and shut all MPI processes down. I have
to tolerate the large loading imbalance (50%) to run
You may download the relevant executables from the following links:
ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64
ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-i386
ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-win32.exe
before using the do_dssp module of Gromacs, ex
Dear gromacs users,
I am running an umbrella pulling to calculate the PMF of a soft protein
adsorbed on surface. Since the protein is soft (easy to deform), I conducted
three pull groups on the COM (center of mass) of three domains of the protein.
The pullings are all along the z axis but on
Hi,
https://onedrive.live.com/redir?resid=990FCE59E48164A4!2572&authkey=!AP82sTNxS6MHgUk&ithint=file%2clog
https://onedrive.live.com/redir?resid=990FCE59E48164A4!2482&authkey=!APLkizOBzXtPHxs&ithint=file%2clog
These are 2 log files. The first one is using 64 cpu cores(64 / 16 = 4
nodes) and 4n
Hi,
Thank you for your answer, could you please give me some more info on where
to find them and how to use them for the whole trajectory?
Cheers,
Nicholas
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
You may use the precompiled dssp executables.
*Thanks and Regards,Bipin Singh*
On Mon, Aug 25, 2014 at 5:31 AM, Nikolaos Michelarakis
wrote:
> Hello,
>
> I am trying to do a secondary structure analysis to get the percentages of
> each secondary structure in my prot
Dear Lovika, Have you looked into atom 19 specifically? Perhaps, changing the coordinate of atom 19 manually, and let it do another minimisation run would solve the issue?Regards,Kester - 원본 메일 -보낸사람 : Lovika Moudgil 받는사람 : 받은날짜 : 2014년 8월 24일(일) 18:28:06제목 : [gmx-users] mdrun err
Hello,
I am trying to do a secondary structure analysis to get the percentages of
each secondary structure in my protein. I know i can use do_dssp but
unfortunately DSSP is not installed on the cluster that i have been using
and i do not have the acess to install it. Any other ways to do it? or
wo
On 8/24/14, 4:36 PM, Xiang Ning wrote:
Dear Justin,
Thanks for your help! It did work when I use grompp to generate tpr file.
However, after obtaining em.tpr file, I want energy minimization of the
membrane+water+ion system, so I typed "mdrun -v -deffnm em", and the outcome
em.gro file lo
On 8/24/14, 8:14 AM, shahab shariati wrote:
Hi
Before, one could search in gromacs mailing list by subject. But, now,
there is not this possibility. Why?
Because Google does the job without the overhead on the Gromacs site:
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
"Brow
On 8/24/14, 5:28 AM, Lovika Moudgil wrote:
Hi everyone ,
Need some help .I have got an error in my mdrun . Upto grompp every thing
was fine but when I give command for mdrun ,It stops with this ...
Steepest Descents:
Tolerance (Fmax) = 1.0e+03
Number of steps=1
S
On 8/24/14, 5:10 AM, Atila Petrosian wrote:
Dear gromacs users
I want to use a new code (g_vesicle_density) in gromacs being in this
address: http://md.chem.rug.nl/~mara/softa/.
There are 2 related files (g_vesicle_density.c and gmx_vesicle_density.c).
I did following steps to use this anal
Dear Justin,
Thanks for your help! It did work when I use grompp to generate tpr file.
However, after obtaining em.tpr file, I want energy minimization of the
membrane+water+ion system, so I typed "mdrun -v -deffnm em", and the outcome
em.gro file looks really weird by using VMD to view. T
On Thu, Aug 21, 2014 at 8:25 PM, Yunlong Liu wrote:
> Hi Roland,
>
> I just compiled the latest gromacs-5.0 version released on Jun 29th. I will
> recompile it as you suggested by using those Flags. It seems like the high
> loading imbalance doesn't affect the performance as well, which is weird.
Hi
Before, one could search in gromacs mailing list by subject. But, now,
there is not this possibility. Why?
Please guide me.
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www
Hi everyone ,
Need some help .I have got an error in my mdrun . Upto grompp every thing
was fine but when I give command for mdrun ,It stops with this ...
Steepest Descents:
Tolerance (Fmax) = 1.0e+03
Number of steps=1
Step= 14, Dmax= 1.2e-06 nm, Epot= 2.08534e+18 F
Dear gromacs users
I want to use a new code (g_vesicle_density) in gromacs being in this
address: http://md.chem.rug.nl/~mara/softa/.
There are 2 related files (g_vesicle_density.c and gmx_vesicle_density.c).
I did following steps to use this analysis for my system:
1) I copied the files (g_ve
31 matches
Mail list logo
