I am sorry There is no "7ws" Its a typographic error. What I wanted to ask
was -
I am comparing two simulations S1 and S2 for contacts at a given cut off
I used g_mdmat and g_hbond to calculate it.
g_hbond outputs: of "-num" and "-hbn" was considered.
1. -hbn output was analysed to calc
Hello Mark
Sorry for the misunderstanding. Actually i did not provide any extra flags
to cmake. I generally edit the CMakeCache.txt file to provide the proper
paths. I somehow felt that was easier to do. I didn't think that could
lead to errors. I have installed gromacs 4.6 on multiple systems usin
On Sat, Mar 2, 2013 at 6:40 PM, Yun Shi wrote:
> Hi all,
>
> I have read http://www.gromacs.org/Documentation/Cut-off_schemes, but
> still unsure about how Verlet works.
>
> "The group cut-off scheme can be combined with a buffered
> pair-list..The Verlet list scheme has buffered neighborlist
By asking how you "calling cmake" I mean that cmake takes a number of
command-line options, and since using those inappropriately (or not calling
the right MPI wrapper compiler) might cause symptoms like yours, we need
more complete information to have a chance of helping solve your problem.
Christ
Gromacs users,
I am trying to run a simulation with a time dependent electric field with
frequency of around 16 GHz in the Z direction. What numbers should I put in
the .mdp file following E-zt: for a field with this frequency? I have looked
at the source code but cannot determine what units the f
On 3/4/13 4:11 PM, Miguel Ángel Mompeán García wrote:
The version I was using this morning was 4.6
In that case, it's probably something worth pursuing. Having the new version
fail when an older version works is curious. Can you please provide all of the
following details:
1. Compilers
The version I was using this morning was 4.6
2013/3/4, Justin Lemkul :
>
>
> On 3/4/13 3:08 PM, Miguel Ángel Mompeán García wrote:
>> I have tried the same issue (same system with same mdp file and same
>> initial configuration as starting structure) and is running without
>> any problems with GRO
Hi,
There are some clarifications needed and as this might help you and other
understand what's going on, I'll take the time to explain things.
Affinity setting is a low-, operating system-level, operation and "locks"
(="pins") threads to physical cores of the CPU preventing the OS from
moving th
On 3/4/13 3:08 PM, Miguel Ángel Mompeán García wrote:
I have tried the same issue (same system with same mdp file and same
initial configuration as starting structure) and is running without
any problems with GROMACS-4.5.5.
Anyone knows what is happening?
You didn't tell us your Gromacs ver
I have tried the same issue (same system with same mdp file and same
initial configuration as starting structure) and is running without
any problems with GROMACS-4.5.5.
Anyone knows what is happening?
2013/3/4, Justin Lemkul :
>
>
> On 3/4/13 8:25 AM, Miguel Ángel Mompeán García wrote:
>> Dear
> OK, but that still might not be fixing the real problem, which might be
> starting with how you are calling cmake in the first place.
>
> Mark
Actually, i called the cmake-2.8.10 which i had installed in my home
directory as the one installed on the cluster was an old version.
so i cd to the cm
On 3/4/13 1:10 PM, Kavyashree M wrote:
On Mon, Mar 4, 2013 at 11:10 PM, Justin Lemkul wrote:
When measuring contacts, you don't measure one group, you measure the
number of contacts that occur between groups A and B, which considers all
atoms in those two groups.
I gave a group of hydrop
On Mon, Mar 4, 2013 at 11:10 PM, Justin Lemkul wrote:
>
> When measuring contacts, you don't measure one group, you measure the
> number of contacts that occur between groups A and B, which considers all
> atoms in those two groups.
>
I gave a group of hydrophobic atoms in both cases
The command
I added this line (CA C Oga_30) to topology file and problem
solved.
Justin are right as usual,
Regards,
Eduardo.
-
Eduardo Villarreal Ramírez
Postdoctoral Research Fellow
Mineralized Tissue Laboratory,
Hospital for Special Surgery.
--
View this
On 3/4/13 12:27 PM, amna khan wrote:
2230 atoms and same as tutorial
I'm assuming that you are using implicit solvent then? Which tutorial are you
referring to?
-Justin
On Mon, Mar 4, 2013 at 9:22 PM, Justin Lemkul wrote:
On 3/4/13 11:20 AM, amna khan wrote:
hi,
i want to ask
On 3/4/13 12:04 PM, Kavyashree M wrote:
Sir,
From Index file which gives the unique contacts -
First section the list of atoms I want to analyse
When measuring contacts, you don't measure one group, you measure the number of
contacts that occur between groups A and B, which considers all
and what about gromacs webserver ?
can i submit all my prepared files there ?
On Mon, Mar 4, 2013 at 10:27 PM, amna khan wrote:
> 2230 atoms and same as tutorial
>
>
>
>
> On Mon, Mar 4, 2013 at 9:22 PM, Justin Lemkul wrote:
>
>>
>>
>> On 3/4/13 11:20 AM, amna khan wrote:
>>
>>> hi,
>>> i want
2230 atoms and same as tutorial
On Mon, Mar 4, 2013 at 9:22 PM, Justin Lemkul wrote:
>
>
> On 3/4/13 11:20 AM, amna khan wrote:
>
>> hi,
>> i want to ask i have i3 laptop
>> i want to run the 1ns simulations
>> how much time it will take ?
>>
>>
> There is no way to tell. The time it takes d
Sir,
>From Index file which gives the unique contacts -
First section the list of atoms I want to analyse
[ C_CA_CB_CD_CD1_CD2_CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_CZ2_CZ3_CH2 ]
second section : the unique contacts of each atoms with others
[ contacts_C_CA_CB_CD_CD1_CD2_CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_CZ2_C
Thanks a lot for the suggestions.
It worked.
On Mon, Mar 4, 2013 at 8:44 PM, Erik Marklund wrote:
> As Justin implied, -merge could potentially make a factor of 2. Try
> g_hbond -nomerge.
>
> Erik
>
>
> On Mar 4, 2013, at 4:02 PM, bipin singh wrote:
>
> Thanks for the reply.
>> The difference
On 3/4/13 11:25 AM, Kavyashree M wrote:
Dear users,
I used the following tool for finding the contacts
g_hbond_46 -f a.xtc -s a.tpr -contact -n a.ndx -r 0.4 -hbm a.xpm -hbn a.ndx
-num a.xvg
From the index file, the number of contacts of each atom was extracted.
This and the
xvg output was co
Dear users,
I used the following tool for finding the contacts
g_hbond_46 -f a.xtc -s a.tpr -contact -n a.ndx -r 0.4 -hbm a.xpm -hbn a.ndx
-num a.xvg
>From the index file, the number of contacts of each atom was extracted.
This and the
xvg output was compared with another simulation.
It was found
On 3/4/13 11:20 AM, amna khan wrote:
hi,
i want to ask i have i3 laptop
i want to run the 1ns simulations
how much time it will take ?
There is no way to tell. The time it takes depends on the size of the system
(number of atoms) and algorithms chosen.
-Justin
--
===
Thank you so much, Justin! Yes, I will do so. :)
Take care.
Best wishes.
--
View this message in context:
http://gromacs.5086.n6.nabble.com/Output-for-rmsd-and-radius-of-gyration-doubts-tp5005881p5006087.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
gmx-users
On 3/4/13 10:37 AM, Ewaru wrote:
Hi Justin,
Thank you for your prompt reply! As this is my first approach to molecular
dynamics, I still have lots of to understand but I'm constantly reading and
trying to work things out. I predicted 2 structures, one using Modeller, and
another one with I-Tas
Hi Justin,
Thank you for your prompt reply! As this is my first approach to molecular
dynamics, I still have lots of to understand but I'm constantly reading and
trying to work things out. I predicted 2 structures, one using Modeller, and
another one with I-Tasser. I followed your very informative
As Justin implied, -merge could potentially make a factor of 2. Try
g_hbond -nomerge.
Erik
On Mar 4, 2013, at 4:02 PM, bipin singh wrote:
Thanks for the reply.
The difference is almost double, through g_hbond the average number of
contacts are 1821 and through g_mindist it is 3643. The calcu
Thanks for the reply.
The difference is almost double, through g_hbond the average number of
contacts are 1821 and through g_mindist it is 3643. The calculation group
does not contains hydrogen atoms.
On Mon, Mar 4, 2013 at 8:14 PM, Justin Lemkul wrote:
>
>
> On 3/4/13 9:08 AM, bipin singh wrot
On 3/4/13 9:49 AM, Ewaru wrote:
Hi Justin,
I tried running the simulation for 10ns and this time, my RMSD graph shows a
stable fluctuation of 0.45nm from 2.5ns to 10ns. The radius of gyration
shows stable fluctuation from 4ns to 10ns around 2.46nm. My doubt is,
shouldn't the RMSD be fluctuatin
Hi Justin,
I tried running the simulation for 10ns and this time, my RMSD graph shows a
stable fluctuation of 0.45nm from 2.5ns to 10ns. The radius of gyration
shows stable fluctuation from 4ns to 10ns around 2.46nm. My doubt is,
shouldn't the RMSD be fluctuating at 0.1nm? Does it mean that my str
On 3/4/13 9:15 AM, Ankita naithani wrote:
Hi,
I recently ran a simulation with the complete structure of my protein
alongwith the ligands. I was running some analysis and was trying out
the Principal component analysis.
I used the g_covar tool to get the eigenvalues and eigenvectors for
protei
On 3/4/13 9:08 AM, bipin singh wrote:
Hi All,
I have a doubt regarding the calculation of number of contacts between two
groups. Because, I am getting different number of contacts calculated
through g_hbond -contact option and g_mindist -on option.
I have used same cutoff for distance (0.6nm)
On 3/4/13 8:25 AM, Miguel Ángel Mompeán García wrote:
Dear gmx users,
I have successfully performed simulations on a charged peptide. I did a
series of mutations and everything had a happy end. Now I have tried
another mutation (just substitution of Asn to Lys) and I am getting the
well-known
On 3/4/13 7:54 AM, mcapar wrote:
Dear GROMACS users,
In gromacs, the default values of the geometrical criterion of H-bond are
0.35 nm and 30 deg for spc water molecules. The acceptor and donor atoms of
H-bond in my system are different than in the water system. Therefore I
think that I should
On 3/4/13 12:50 AM, Jeff Yew wrote:
If I have water and solvent, and I only want to apply a short range switching
function to the water - water interactions (not solvent - solvent or water -
solvent), is it possible in Gromacs? I am interested in reproducing TIP4P-EW
water.
If I add "coulom
Hi All,
I have a doubt regarding the calculation of number of contacts between two
groups. Because, I am getting different number of contacts calculated
through g_hbond -contact option and g_mindist -on option.
I have used same cutoff for distance (0.6nm) in both the cases.
--
*--
Dear gmx users,
I have successfully performed simulations on a charged peptide. I did a
series of mutations and everything had a happy end. Now I have tried
another mutation (just substitution of Asn to Lys) and I am getting the
well-known
"X particles communicated to PME node Y are more than a c
Dear GROMACS users,
In gromacs, the default values of the geometrical criterion of H-bond are
0.35 nm and 30 deg for spc water molecules. The acceptor and donor atoms of
H-bond in my system are different than in the water system. Therefore I
think that I should use suitable D-A distance and H-D-A
On Mon, Mar 4, 2013 at 6:02 AM, Reid Van Lehn wrote:
> Hello users,
>
> I ran into a bug I do not understand today upon upgrading from v. 4.5.5 to
> v 4.6. I'm using older 8 core Intel Xeon E5430 machines, and when I
> submitted a job for 8 cores to one of the nodes I received the following
> err
OK, but that still might not be fixing the real problem, which might be
starting with how you are calling cmake in the first place.
Mark
On Sat, Mar 2, 2013 at 7:20 AM, Abhishek Acharya wrote:
> >> Date: Fri, 1 Mar 2013 23:59:36 +0530
> >> From: "Abhishek Acharya"
> >> Subject: [gmx-users] Inst
Hi Gromacs user,
when I try to extend on of my simulations with
mdrun -deffnm pdz_cis_NVT_disre_equi_3 -cpi
pdz_cis_NVT_disre_equi_3.cpt -append
I get the following error
Fatal error:
Count mismatch for state entry disre_rm3tav, code count is 0, file count
is 13
and have no idea whats w
41 matches
Mail list logo
