Over the past couple days I've attempted to implement the water model
developed by Ishiyama & Morita (J. Phys. Chem. C 2007, 111, 721-737) using a
combination of the shell polarization technique and tabulated potentials for
the bonded terms, among other things. Before elaborating below, the
documen
I can help with only some of this...
- Original Message -
From: Eric Shamay
Date: Wednesday, October 6, 2010 18:35
Subject: [gmx-users] New shell water model, tabulated bonding interactions, and
the documentation.
To: gmx-users@gromacs.org
> Over the past couple days I've attempted to i
Hi,
Estimate for the relative computational load of the PME mesh part: 0.33
How do I set how many nodes I should use?
#PBS -l nodes=12:ppn=4
What if the PME mesh part has different values?
is it okay? Before I did those kind of very blindly, just based on the most
nodes I can use to hopefully
I think the PME mesh part is ok and it should be less than 0.5 always.
Regarding the nodes ask your administrator how many ppn one node have.
example
suppose if one node has 6 ppn then 12 nodes will have 72ppn which is
sufficient to run md.
hope the above explanation helps you.
Regards
Vinoth
O
I think I know how many ppn one nodes have. :-)
My question was that the number of ppn has something to do with the PME mesh
part number or not?
Why sometimes I had a big load imbalance.
Thanks and best regards,
lina
From: gmx-users-boun...@gromacs.org [gmx-us
- Original Message -
From: #ZHAO LINA#
Date: Wednesday, October 6, 2010 19:44
Subject: [gmx-users] How can I best setup the nodes number
To: "gmx-users@gromacs.org"
P {margin-top:0;margin-bottom:0;}
---
|
> Hi,
>
> Es
Dear Igor,
Your output look _very_ weird, it seems as if CMake internal
variable(s) were not initialized, which I have no clue how could have
happened - the build generator works just fine for me. The only thing
I can think of is that maybe your CMakeCache is corrupted.
Could you please rerun cma
Hi,
> Does anyone have an idea about what time the Gmx 4.5.2 will be released?
Soon, if everything goes well in a matter of days.
> And in 4.5.2, would the modified tip5p.itp in charmm27 force field be the
> same as that in current git version?
The git branch release-4-5-patches is the branch
> Date: Wed, 6 Oct 2010 11:53:56 +0200
> Subject: Re: [gmx-users] charmm tip5p in Gmx 4.5.2
> From: szilard.p...@cbr.su.se
> To: gmx-users@gromacs.org
>
> Hi,
>
> > Does anyone have an idea about what time the Gmx 4.5.2 will be released?
>
> Soon, if everything goes well in a matter of days.
Dear friends
I would like to get the water molecule residue no which is near a protein
molecule active site and its residence time could anyone please help me in this
regard
Thanking you
E R Azhagiya singam
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman
babu gokul skrev 2010-10-06 12.27:
Dear friends
I would like to get the water molecule residue no which is near a
protein molecule active site and its residence time could anyone
please help me in this regard
Thanking you
E R Azhagiya singam
Try g_dist and/or g_hbond.
--
-
Dear friends,
please tell me, what are the possible reasons for the system total charge in
not zero and the need to neutralise it in MD simulation of the proteins.
--
Anil R.Mhashal
Research fellow
Physical Chemistry Division
National Chemical Laboratory
Pune
--
gmx-users mailing listgmx-us
Hi Mark,
Thank you for your help. Your reply gave me some hints. Firstly, I
will check again whether thread caused the problem. Then check the
requirements for code to work with threading.
The thing worries me on thread is that, Gromacs uses its own library
not the common OpenMP to manipulate thr
Hi all,
Just to let everyone know that I have uploaded my conversion of the
CHARMM36 force field to the GROMACS website. If you are going to use
these files then please have a read of the forcefield.doc file for some
more information. These lipid parameters have been checked against the
conve
Hello,
To investigate the secondary structure I issued the do_dssp command as
follows:
do_dssp_d_mpi -f AFPIII_Ih0001_81_93_NpT265.xtc -s
AFPIII_Ih0001_81_93_NpT265_1.tpr -o AFPIII_Ih0001_81_93_NpT265 -ssdump
AFPIII_Ih0001_81_93_NpT265
Then, I had read somewhere in the archive to select the alph
Paymon Pirzadeh wrote:
Hello,
To investigate the secondary structure I issued the do_dssp command as
follows:
do_dssp_d_mpi -f AFPIII_Ih0001_81_93_NpT265.xtc -s
AFPIII_Ih0001_81_93_NpT265_1.tpr -o AFPIII_Ih0001_81_93_NpT265 -ssdump
AFPIII_Ih0001_81_93_NpT265
Then, I had read somewhere in the
Dear Justin,
Thanks a lot. Your comment was very instructive. So, I use Mainchain
(group 5) for future.
Paymon
On Wed, 2010-10-06 at 12:41 -0400, Justin A. Lemkul wrote:
>
> Paymon Pirzadeh wrote:
> > Hello,
> > To investigate the secondary structure I issued the do_dssp command as
> > follows:
Dear Anil:
If the charge is integer, I believe this depends only on your protein,
and you are the only one who knows the answer. If the charge is not
integer, then these are rounding errors.
--
Dr. Vitaly V. Chaban
Department of Chemistry
University of Rochester
Rochester, NY 14627-0216
United S
Hello,
I want to check the secondary structure of protein at particular residues.
Since dssp needs all main chain atoms, does the following command at the
make_ndx prompt makes the correct index file?
5 | r 1 | r 10-11 |r 14-17 | r 20-21 | r 26-32 | r 42 | r 45
(Main chain atom of particular
Paymon Pirzadeh wrote:
Hello, I want to check the secondary structure of protein at particular
residues. Since dssp needs all main chain atoms, does the following command
at the make_ndx prompt makes the correct index file?
You can answer that yourself by looking at the resulting index file.
Hi Berk,
Thanks for your reply.
Actually I followed the fws-peptide simulation in Dr. JE Kerrigan's tutorial,
but in charmm27 force field with tip5p water.
Before several warnings in the simulation step, I found that even in energy
minimization step the protein cannot be settled. I sent my m
Justin,
I produced the index file based on your suggestion, but when I ran the
do_dssp, a completely different result was spit out comparing to what
the whole protein analysis had given. Any ideas on why that might have
happened?
Paymon
On Wed, 2010-10-06 at 14:42 -0400, Justin A. Lemkul wrote:
>
Paymon Pirzadeh wrote:
Justin,
I produced the index file based on your suggestion, but when I ran the
do_dssp, a completely different result was spit out comparing to what
the whole protein analysis had given. Any ideas on why that might have
happened?
That depends on what "completely differ
Yao Yao wrote:
Hi Berk,
Thanks for your reply.
Actually I followed the fws-peptide simulation in Dr. JE Kerrigan's tutorial,
but in charmm27 force field with tip5p water.
Before several warnings in the simulation step, I found that even in energy
minimization step the protein cannot be settl
I assumption was that when provide the index file, do_dssp will do the
analysis for the protein but prints out the results only for the
designated residues. All I wanted was a better resolution on the final
xpm plot to see the secondary structure of the protein at those residues
of interest. Any su
Paymon Pirzadeh wrote:
I assumption was that when provide the index file, do_dssp will do the
analysis for the protein but prints out the results only for the
designated residues. All I wanted was a better resolution on the final
When prompted for only one group, that group is used for calcul
- Original Message -
From: Vitaly Chaban
Date: Thursday, October 7, 2010 3:53
Subject: [gmx-users] Re: About the charge
To: gmx-users@gromacs.org
> Dear Anil:
>
> If the charge is integer, I believe this depends only on your protein,
> and you are the only one who knows the answer. If
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