Could you provide more information?
>3. Weird error message from QM/MM run. (yoochan,myung)
>4. Re: Re: Re: Fw: Re: Polymer-protein problem (Mark Abraham)
>5. Re: gas adsorption on CNT (Mark Abraham)
>6. simulation crash with GROMOS96 force field (Vitaly V. Chaban)
>
--
gmx-use
HI Tsjerk,
Thanks for your reply. But, I can't see if it is going suddenly or
gradually.
What i can see is the ligand is away from the molecule after editing the gro
file with PRODRG output.
It seems liek PRODRG has modified the co-ordinates that places ligand away
from the protein.
~Vivek
2010/1
Hi Alexandar,
I redirected my answer to the gmx-users mailing list so it's available to all
users.
23 jan 2010 kl. 22.41 skrev Alexandar T Tzanov:
> Hi Par,
>
> I downloaded your 'Charmm to Gromacs port v1.1" and tried it on my simple
> system - NATMA (ACE-TRP-NAC total 36 atoms). I used
Hi,
>> ---
>> Program pdb2gmx, VERSION 4.0.7
>> Source code file: resall.c, line: 344
>>
>> Fatal error:
>> in .rtp file in residue cmap at line:
>> -C N CA C +N
>> :q!
>> ---
Dear all,
I am using MD simulation of a protein on Silicon nitride surface. The
surface has been created using VMD and tcl script (ref. bionano
tutorial).The protein+surface complex also has been generated using
VMD.Using that PDB file I have done md simulation in gromacs. One itp file
for silicon
Hi Justin,
I think you did a great job with that tutorial, a lot of people will
benefit from it. I have just 2 additional suggestions:
1) Maybe you can comment on the issue of equilibration, especially since
you took your initial frames from a non-equilibrium pulling. In such
cases you proba
Hi all,
I am new to gmx. I want to use potassium ions in my system. But grompp gives
me only error. So I go through ffG53a6.atp, but find no atom type for
potassium.
Is this normal or I made some mistakes? If this is normal, how can I use
potassium ion with ffG53a6?
Thanks
Terry
--
gmx-users m
Hi,
>>> ---
>>> Program pdb2gmx, VERSION 4.0.7
>>> Source code file: resall.c, line: 344
>>>
>>> Fatal error:
>>> in .rtp file in residue cmap at line:
>>> -C N CA C +N
>>> :q!
>>> -
Hi Pär,
I actually refered to the .rtp file. I think that the edit was there.
Cheers,
Tsjerk
On Mon, Jan 25, 2010 at 12:24 PM, Pär Bjelkmar wrote:
> Hi,
---
Program pdb2gmx, VERSION 4.0.7
Source code file: resall.c, line: 344
>
Kothai Thiruvengadam wrote:
Dear all,
I am using MD simulation of a protein on Silicon nitride surface. The
surface has been created using VMD and tcl script (ref. bionano
tutorial).The protein+surface complex also has been generated using
VMD.Using that PDB file I have done md simulation in
Dear All,
I was trying to calculate diffusion of water molecule in a membrane
channel protein by g_msd utility of gromacs.
First I have identified channel waters which reside inside the channel
for 500ps (5000ps-5500ps simulation time).
Letter I have made a index file specifying these water mole
Hi all,
For a future project, I would like to use gromacs for simulations with the
CHARMM force field. I am aware that the CHARMM ff is not yet officially
supported by gromacs, even if a paper about this port will be published
soon. By reading the mailing list, I understand that a beta versio
Hi,
i want to simulate 2 parallel plates (each composed of single atoms with
equal spacing , for example 2X2 atoms plate)
i want to simulate them such that they are parallel to each other and can
move only along one axis (for that i used posre.itp..)
what is the best best way to prevent them from
Dear Users,
Re tutorial
http://www.nmr.chem.uu.nl/~tsjerk/course/md-tutorial/
After running comand:
grompp -v -f pr.mdp -c 1LW9-EM-solvated.gro -p 1LW9.top -o 1LW9-PR.tpr
and
mdrun -v -deffnm 1LW9-PR (gave message Routine should not have been called:
Hi,
there is currently no web-interface on the official git server. Thus
repo.or.wz is probably the best solution.
I checked that http://repo.or.cz/w/gromacs.git/snapshot/HEAD.tar.gz is
up-to-date.
Roland
On Tue, Feb 23, 2010 at 8:31 AM, intra\sa175950 wrote:
> Hi all,
>
>
>
> For a future pro
Hi David,
Always check which version a tutorial is written for. And also always
mention which version you're running when posting a question/issue to
the list. Now, with this error, I know you're running the (broken) GMX
3.3.2. The tutorial was written for 3.3.1, but will also work with
3.3.3.
Ch
> 1. No problem at all in vacuo? That with a 1 fs timestep and the sd
> integrator? Strange then that your molecule is ok and the water is ok,
> but they are unstable together. Perhaps your'e not getting any LJ
> interactions (or not correct ones) between your solute and water? That's
> where I wou
Vitaly V. Chaban wrote:
1. No problem at all in vacuo? That with a 1 fs timestep and the sd
integrator? Strange then that your molecule is ok and the water is ok,
but they are unstable together. Perhaps your'e not getting any LJ
interactions (or not correct ones) between your solute and water?
Please find below
===
integrator = md
; Start time and timestep in ps
tinit= 0
dt = 0.001
nsteps = 100
; For exact run continuation or redoing part of a run
init_step= 0
; mode
Vitaly V. Chaban wrote:
There are several potential problems with your .mdp file, mostly due to
parameters that seem inappropriate for use with Gromos96.
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 50
This updating is very infrequent. Usually one s
>
> This updating is very infrequent. Usually one sees a value of 5-10 here
> (usually 5 for Gromos96). If your neighborlist is updated infrequently, you
> can
> have problems (poor energy conservation and perhaps incorrect calculation of
> interactions). Perhaps this is why your short timestep
#
IEEE WETICE 2010
1st International Workshop on
Collaborative Modeling and Simulation
CALL FOR PAPERS
#
June 28 - June
Dear amir:
You have 2 issues:
1. maintain planar plates
2. inhibit plate rotation.
I think that the planarity is actually going to be a bigger problem
for you (unless of course you want your plates to be able to bend).
Position restraints in the relevant dimensions seems like a reasonable
Hi,
i want to simulate 2 parallel plates (each composed of single atoms with
equal spacing , for example 2X2 atoms plate)
i want to simulate them such that they are parallel to each other and can
move only along one axis (for that i used posre.itp..)
what is the best best way to prevent them from
24 matches
Mail list logo
