I extended my simulation of a free protein from 100ns to 150ns.
Corresponding files are extend.gro and extend.xtc.
I applied pbc conditions and my new xtc s newmd.xtc.
I tried to visualise my trajectory in vmd
I uploaded the extend.gro file and loaded newmd.xtc in gro file. But I
couldn't
Thank you,
Best,
*Lan Hoa*
2017-06-15 17:02 GMT-05:00 Mark Abraham :
> Hi,
>
> Those are simply fields separated by whitespace. Columns not relevant.
>
> Mark
>
> On Thu, 15 Jun 2017 22:10 lan hoa Trinh wrote:
>
> > Dear Gromacs society,
> > I
kindly tell me sir how i can i add residue
On Thu, Jun 15, 2017 at 2:04 AM, Rana Rehan Khalid
wrote:
> thanks justin
> actually i want to know that how these values of column (atom name, type,
> charge and charge group) we obtain for oxygen bonded with heme fe. is there
>
Hi,
Those are freely available to register, though I don't have a link to hand.
Mark
On Fri, 16 Jun 2017 00:58 Charles Laughton <
charles.laugh...@nottingham.ac.uk> wrote:
> Hi Mark,
>
> Redmine.gromacs.org asks me for a username and password – I have neither.
>
> Regards,
>
> Charlie
>
>
> On
Hi,
Those are simply fields separated by whitespace. Columns not relevant.
Mark
On Thu, 15 Jun 2017 22:10 lan hoa Trinh wrote:
> Dear Gromacs society,
> I wonder if there is the default for the space between the columns in the
> topology file, for example:
> [ bonds ]
>
Hi Mark,
Redmine.gromacs.org asks me for a username and password – I have neither.
Regards,
Charlie
On 15/06/2017, 19:10, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
behalf of Mark Abraham"
Dear Gromacs society,
I wonder if there is the default for the space between the columns in the
topology file, for example:
[ bonds ]
;ai aj funcr0(nm) Kb
12 1 3.805916447e-01 2.0e+04
23 1 3.788218579e-01 2.0e+04
3
Dear Yogesh:
you either need to make the system larger in the dimension(s) of your pulling
or you need to not pull out to such a far distance. Once you straighten that
out, and if the lincs problems remain, then we can tackle that separately.
What are your mdp options for pulling? Maybe you
Hi,
Redmine.gromacs.org is the place. Please add enough inputs to reproduce the
problem!
Mark
On Thu, 15 Jun 2017 20:42 Charles Laughton <
charles.laugh...@nottingham.ac.uk> wrote:
> Hi Carsten,
>
> Can you explain how I file a bug report? Do I need to be subscribed to the
> gmx-developers
Hi Carsten,
Can you explain how I file a bug report? Do I need to be subscribed to the
gmx-developers list or something?
Regards,
Charlie
On 15/06/2017, 13:50, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
behalf of Kutzner, Carsten"
Hi there,
I am new to GROMACS, went through Lysozeme in Water tutorial and everything
runs smoothly.
I then tried to immobilize all heavy atoms (except H) in md.mdp file by
specifying freezegrps = Protein-H ; Freeze all heavy
atoms
freezedim= Y Y Y ;
Hi Mark,
Great! Thanks a lot. I try with the g96 format.
Best, -Yu
2017-06-15 15:04 GMT+01:00 Mark Abraham :
> Hi,
>
> Yes g96 is a good format for that
>
> Mark
>
> On Thu, 15 Jun 2017 14:38 Yu Ogawa wrote:
>
> > Hi Mark,
> > Thanks for suggestions.
Hi,
You need also the development library part for your x system, so it can be
compiled against. Often in a different but related download.
Mark
On Thu, 15 Jun 2017 16:14 Karchevskaya, Anastasia <
anastasia.karchevskaya...@ucl.ac.uk> wrote:
> Dear Gromacs Users,
>
> I can’t run ngmx.
>
>
Dear Gromacs Users,
I can’t run ngmx.
Gromacs version 4-6-7; tried to re-install already.
Machine: Mac (OS Sierra)
X11/XQuartz: XQuartz 2.7.11 (xorg-server 1.18.4)
Lesstif: lesstif 0.95.2 Installed with brew
What else should I do to make it work? What am I doing wrong? Thank you
Ana
--
Hi,
Yes g96 is a good format for that
Mark
On Thu, 15 Jun 2017 14:38 Yu Ogawa wrote:
> Hi Mark,
> Thanks for suggestions. I will take a look at the g96 format.
> I try to deform a part of polymer crystal with a small displacement, and
> then relax the structure in MD while
Hi Experts,
I am doing simulation for permeability calculation.
In my simulation, water molecule is constrained (inside the Bilayer) at fixed
distance from centre of the Bilayer. And another constrained in bulk water. I
am doing equilibration with V-rescale(thermostat) and berendsen(for
Hi Charlie,
I just made a quick check with 5.1 and 2016 and I also see the problem that you
described. For me IMD works with 5.1, but not with 2016, but I don't know why.
Could you file a bug report?
Thank you,
Carsten
> On 14. Jun 2017, at 18:05, Charles Laughton
>
So the following question, if I want to change a few residues in a system that
is already made (equilibrated, a protein in a lipid membrane), how should i go
about that? What would be the protocol?
I did it this way -> i first made a pdb out of the last frame (changed the 3
residues in
Hi Mark,
Thanks for suggestions. I will take a look at the g96 format.
I try to deform a part of polymer crystal with a small displacement, and
then relax the structure in MD while keeping the displacement by
constraint. As the displacement can be very small, I want to have an input
structure file
Hi,
Usually one doesn't need a higher precision text file. The g96 format does
work for this, but you should probably be using a real trajectory or
checkpoint format for whatever you are trying to do. That would have been
good to describe, rather than assuming the form of the solution ;-)
Mark
Hi,
Check again the mdp options. Zero may not be the right choice for all of
them
Mark
On Thu, 15 Jun 2017 13:56 Linus Johannissen <
linus.johannis...@manchester.ac.uk> wrote:
> Thanks Justin,
>
> I'm using Gromacs 4.6.1. I don't think changing energygrps is going to
> change anything as I
Thanks Justin,
I'm using Gromacs 4.6.1. I don't think changing energygrps is going to change
anything as I have the same problem in the energy minimisation (zero LJ (SR)
and Coulomb (SR) energies). However, I found that if the simulation seems to
run fine if I use a cutoff of 999 instead of 0.
Hi Eric,
Thanks for replying.
I may be wrong, but what I understand from the online manual is that we
have a higher precision in MD calculation (as in trr file). I am not sure
if grompp recognizes a higher precision than 3 decimal places.
When I did editconf with a gro file with higher precision
Hello Yu,
Read this carefully.
http://manual.gromacs.org/online/gro.html
As far as I know, Gromacs will accept gro files with high precision if the
input file follows this format.
Best,
Eric
> On Jun 15, 2017, at 4:33 AM, Yu Ogawa wrote:
>
> Hello gmx users,
> Can we
Hello gmx users,
Can we increase a precision of input structure file more than 3 decimal
places?
Thank you for your help!
Yu
--
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
The file rms.xvg contains only RMSD values against the reference PDB structure;
what I need to know is the contents of RMSD matrix between 2 trajectories.
Qing
At 2017-06-15 15:17:08, "Dd H" wrote:
>I think this link should be helpful.
*Dear Gromacs users,*
I am trying to simulate a peptide nanutube composed by 8
cyclics.When I execute pdb2gmx with the options -missing and -ter
(selecting manually None), as I have seen in the Gromacs list, I get
this error:
pdb2gmx -f tube.pdb -ter -missing -ignh8 out of 8 lines of
Hi Experts,
I am doing simulation for permeability calculation.
In my simulation, water molecule is constrained (inside the Bilayer) at
fixed distance from centre of the Bilayer. And another constrained in bulk
water. I am doing equilibration with V-rescale(thermostat) and berendsen(for
Hi,
How to run potential energy surface scan for a molecule using gromacs?.
What are the steps?
Thanks,
Neha
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Gromacs Users mailing list
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http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read
I think this link should be helpful.
http://manual.gromacs.org/programs/gmx-rms.html
You can have a look at rms.xvg file, it contains rmsd values.
Best regards,
Dading Huang
On Wed, Jun 14, 2017 at 7:05 PM, Qing Lv wrote:
> I generated a .dat file with the following
thanks justin
actually i want to know that how these values of column (atom name, type,
charge and charge group) we obtain for oxygen bonded with heme fe. is there
any program through which i find the parameter file for oxygen with heme
and nitric oxide with heme iron. if i just add the atom name
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