Hi,
thanks to Justin for the pointer to the list archive I searched before
with net charge, but without getting useful results. For the sake of
clarity, I am not referring to the neutralizing plasma or neutralizing
background charge used implicitly with PME, but to an additional
net-charge
Hi Tarak,
I have had the same problem. As far as I know, it is not possible to use
Nose-Hoover + Parrinello-Rahman in combination with the md-vv integrator.
I am using md (leap-frog) in combination with Nose-Hoover +
Parrinello-Rahman, this is working fine.
I guess it would be great to get a
Hi Tuba,
I guess you have to create an index for each peptide and then
extracting covariance matrix on each peptide using the new indexes.
Francesco
2012/11/6 Tuba Kilinc tkil...@gmail.com
hi all,
i would like to apply PCA (principal component analysis) for my peptides
that i simulated. i
On 11/6/12 3:56 AM, dakoenig wrote:
Hi Tarak,
I have had the same problem. As far as I know, it is not possible to use
Nose-Hoover + Parrinello-Rahman in combination with the md-vv integrator.
I am using md (leap-frog) in combination with Nose-Hoover +
Parrinello-Rahman, this is working
Dear Justin,
Thank you for the answer.
I'm using OPLS force field but I calculated the partial charges of the atoms
from the HF geometry optimization.
Do you have any idea if I should arrange the charge groups in this case or
not?
Regards,
Akn.
--
View this message in context:
Thank you for the reply,
Figured. Needless to say though, the software using the pulled gives about the
same as by hand (although diffusion constants are also guessed but fit into
what the computer calculates as compared on a scale of lysozyme,,, xxx, Fab
fragments) but can not do the
Hi,
are you sure that you want to have pull_dim = Y Y Y (which is the
default)? When you want to pull only in z direction, I would use
pull_dim = N N Y. Otherwise, your z coordinate is not your reaction
coordinate.
If you want to pull in 3 dimensions you probably want to use
On 11/5/12 11:25 PM, benjfitz wrote:
Justin, thank you for reminding me that I need to adhere to sane parameters.
I do have a few clarifying points, as it were. I tried these simulations
again, but with a larger box and 0.9 nm cutoffs, and received a segfault at
the same simulation time.
The
On 11/5/12 11:52 PM, harshaljain950 wrote:
Dear all,
I am a final year undergrauate student and a novice in GROMACS.
I want 3-4 layers of Carbon atoms to be added one over the other in my box
starting from Z=0 to Z=(3-4 carbon diameter). How can I do that. Please help
me out
genconf
On 11/6/12 6:56 AM, akn wrote:
Dear Justin,
Thank you for the answer.
I'm using OPLS force field but I calculated the partial charges of the atoms
from the HF geometry optimization.
Do you have any idea if I should arrange the charge groups in this case or
not?
My intuition says that a
Thanks for the suggestion, I should have mentioned Tcoupl and Pcoupl in my
previous post. I changed them from Nose-Hoover/Parrinello-Rahman to
V-rescale/Berendsen and one permutation mixing the two, but it crashed all
the same.
The nodes have at least 8 GB of ram and free -m shows that I'm not
On 11/6/12 9:01 AM, benjfitz wrote:
Thanks for the suggestion, I should have mentioned Tcoupl and Pcoupl in my
previous post. I changed them from Nose-Hoover/Parrinello-Rahman to
V-rescale/Berendsen and one permutation mixing the two, but it crashed all
the same.
The nodes have at least 8 GB
Hi, thanks for your response,
Since I'm using pull_geometry=position I was under the impression that
defining pull_dim was not necessary.
Instead, I defined pull_vec to specify that the protein should be pulled
along 0 0 1
I was previously using pull_geometry=distance with pull_dim= N N Y but
use make_ndx to create a new group, then use the -n index.ndx option with
g_covar
Date: Tue, 6 Nov 2012 09:58:51 +0200
From: tkil...@gmail.com
To: gmx-users@gromacs.org
Subject: [gmx-users] PCA
hi all,
i would like to apply PCA (principal component analysis) for my peptides
that i
On 11/6/12 12:12 PM, Ali Alizadeh wrote:
Dear All users
1- Do these parameters strongly impact on my final results?
rlist
rcoulomb
rvdw
Yes, potentially very strongly.
2- Are these parameters independent from type of system and only
dependent to type of the force fields?
Yes.
3- I
I wasn't outputting an arbitrary configuration - the timestep at 1000 was the
last frame of my equilibration.
On 5 November 2012 16:37, Justin Lemkul jalem...@vt.edu wrote:
On 11/5/12 7:25 PM, rainy908 wrote:
Fellow Gromacs users:
Suppose I run a 1 ns equilibration on my protein system prior
On 11/6/12 1:14 PM, rainy908 wrote:
I wasn't outputting an arbitrary configuration - the timestep at 1000 was the
last frame of my equilibration.
I was replying to your question regarding the choice of configuration, whether
or not you needed to do any sort of RMSD clustering.
-Justin
On 11/6/12 1:21 PM, Ali Alizadeh wrote:
Dear Justin
Thank you for your reply
On 11/6/12 12:12 PM, Ali Alizadeh wrote:
Dear All users
1- Do these parameters strongly impact on my final results?
rlist
rcoulomb
rvdw
Yes, potentially very strongly.
2- Are these parameters
I was making a clarification regarding the equilibration, not the RMSD
clustering.
On 6 November 2012 10:16, Justin Lemkul jalem...@vt.edu wrote:
On 11/6/12 1:14 PM, rainy908 wrote:
I wasn't outputting an arbitrary configuration - the timestep at 1000 was the
last frame of my equilibration.
On 11/6/12 1:37 PM, Ali Alizadeh wrote:
Dear All users
1- I got an error when i wanted to perform EM, my emtol = 100 but it
did not converge
Water molecule starting at atom 5113 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
...
I saw the pdb files
On 11/6/12 2:10 PM, Ali Alizadeh wrote:
Dear Justin
What did you do to fix the problem?
it converged, in next step i got em.gro as a input file and perform
another EM with emtol=900
It converged , and i continued to emtol=100
Did it work the second time?
Yes, But i
On 11/6/12 2:19 PM, Ali Alizadeh wrote:
Dear Justin
I added this line to my minim.mdp file and i solved the error,
define = -DFLEXIBLE
Why did this line affect to em convergence?
Do you know what this setting does?
-Justin
--
Justin A.
Hi all,
I'm trying to build the mdrun binary for the BGQ system with the following
commands (current dir is /scratch/dlin13/gromacs/gromacs-4.5.5/backend) :
../configure --prefix=/scratch/dlin13/gromacs/gromacs-4.5.5/backend \
--build=powerpc64-bgq-linux \
On 11/6/12 10:42 PM, Ali Alizadeh wrote:
Dear All users
I used OPLS ff for my system and I did not break my bonds,
When i use gromos96 45a3 after minimizing my bonds break(i can see
em.gro) but i do not get any errors in this step
Bonds do not break during MD. Probably what you're seeing
Dear gmx users:
So sorry for bother you. Does any one know what algorithm g_sas
use? There is no information about algorithm in help file, man page,
and code. I think gromos use naccess method but not sure gromacs use
the same one.
Regards
ZhiGuang Jia
--
gmx-users mailing list
On 11/7/12 1:18 AM, jia jia wrote:
Dear gmx users:
So sorry for bother you. Does any one know what algorithm g_sas
use? There is no information about algorithm in help file, man page,
and code. I think gromos use naccess method but not sure gromacs use
the same one.
References are
Thanks! I've checked gromacs v 4.5.5 and got it.
Seems all version before 4.0.5 doen't have that information..
Cheers
Guang
2012/11/7, Justin Lemkul jalem...@vt.edu:
On 11/7/12 1:18 AM, jia jia wrote:
Dear gmx users:
So sorry for bother you. Does any one know what algorithm g_sas
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