Hi everyone,
I am sending this email again hoping for any quick input for my question.
I have been trying to set up an "infinitely" hard potential wall.
I tried to use the available wall options and could not really get it to do
what i needed. I wanted a steep repulsive potential but when i cr
On Thu, Oct 22, 2009 at 9:53 AM, S hv wrote:
> Hi,
>
> I am currently working with peptide/lipids interactions using the martini
> force field. I want to built a bacterial membrane, so I trying to find the
> topology of the POPG lipid but until now without success.
>
>
> In the martini_v2.0_li
Erik Marklund wrote:
Hi users,
I have simulated a box of NVT-water, more specifically the flexible
urey-bradley-like TIPS-reparametrisation by Dang and Pettitt (1987).
What I notice is that the diffusion coefficient increases when I
calculate it from a longer snippet from my trajectory. If I
Mark Abraham ha scritto:
> ms wrote:
>> Ok, the problem is that I want to re-implement a quite minimal
>> coarse-grained FF (so no explicit solvent etc.) and a directional
>> interaction would be useful.
>
> Well you should consider alternative software, then.
I see. I wonder if patching gmx to d
Hi,
I am currently working with peptide/lipids interactions using the martini force
field. I want to built a bacterial membrane, so I trying to find the
topology of the POPG lipid but until now without success.
In the martini_v2.0_lipids.itp file, the PG lipids are no included. I have seen
While using g_wham to obtain a PMF from umbrella sampling simulations I came
up with the following problem. I have simulated my windows with a 0.1nm
difference between structures starting from the initial position where my
dimer is equilibrated and ending 0.5nm farther than what the lennard jones
a
Hello,
I've compiled gromacs on BlueGene/P system and it would be great if some
one send me an input and tell me what is the performance of the gromacs
runing this job on another BG/P system.
Thank you in advance!
Peicho.
___
gmx-users mailing list
Hi users,
I have simulated a box of NVT-water, more specifically the flexible
urey-bradley-like TIPS-reparametrisation by Dang and Pettitt (1987).
What I notice is that the diffusion coefficient increases when I
calculate it from a longer snippet from my trajectory. If I use only 100
ps; star
Hello. I am working on some free energy calculations for a protein-protein
interaction. I decided to try and reproduce the delta G for the well-studied
barnase-barstar interaction before I work with a novel system. I am running the
FE calculations on the barnase-barstar complex, and the barnase
Dear Gmx users,
Does any one know how to convert itp/pdb file to dlpoly FIELD format?? Any
information regarding that will really appreciate... Please let me know if
you have any reference/script ... to make my FIELD file for dlpoly since I
am trying that for a while... Many Thanks in Advance/Jamie
>1. Re: COM removal type angular with PBC? (Mark Abraham)
>> Dear All,
>> I'm attempting to simulate a dimeric protein in an explicit
>> bilayer/water environment. I'd like to remove the translation & rotation
>> of one protomer relative to the other, so that one protomer is able to
>>
ram bio wrote:
Dear Mark,
Thanks and you are right, that when a docked complex (protein +
ligand) is simulated, the favorable ligand binding poses can be
predicted using MD (longer runs). What I am trying to do here
presently is not to simulate a docked complex, but to generate a
modelled protei
Dear Mark,
Thanks and you are right, that when a docked complex (protein +
ligand) is simulated, the favorable ligand binding poses can be
predicted using MD (longer runs). What I am trying to do here
presently is not to simulate a docked complex, but to generate a
modelled protein lowest energy c
Carla Jamous wrote:
Dear Alan,
if I completely understood how acpypi works, it seems that it generates
the topology parameters from the pdb file of the molecule.
But the problem is that I have the topology parameters (my angles, bond
distances and dihedrals) and want to implement them in Gromac
Dear Alan,
if I completely understood how acpypi works, it seems that it generates the
topology parameters from the pdb file of the molecule.
But the problem is that I have the topology parameters (my angles, bond
distances and dihedrals) and want to implement them in Gromacs, so actually
I want to
ram bio wrote:
Dear Mark,
You mean that I should consider a configuration with the lowest total
energy for docking studies..Please clarify and suggest me.
If you read your docking program's documentation, they are using their
"energy" as a some kind of approximation to a free energy of ligand
Thanks Mark and Omer for your comments - I have really learning a lot on
RDF today based on your input!
From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Omer Markovitch
Sent: Thursday, October 22, 2009 3:49 PM
To: Discussion list for GROMACS users
Subj
On Oct 22, 2009, at 11:54 AM, albita...@virgilio.it wrote:
Hi,
I'm checking my system and topology but I noticed a quite weird
behaviour in
this concern.
When I run my simulation starting from a pre-optimized geometry, the
simulation
crashes with segmentation fault.
what do you mean by p
Hi,
I'm checking my system and topology but I noticed a quite weird behaviour in
this concern.
When I run my simulation starting from a pre-optimized geometry, the simulation
crashes with segmentation fault.
On the other hand, when I run the same simulation but starting from the
geometry I generate
Dear Mark,
You mean that I should consider a configuration with the lowest total
energy for docking studies..Please clarify and suggest me.
Thanks,
Ram
On Thu, Oct 22, 2009 at 3:56 AM, Mark Abraham wrote:
> ram bio wrote:
>>
>> Dear Justin,
>>
>> Thanks for the suggestion and advice.
>> As i h
Kukol, Andreas wrote:
Hi,
Finally I found the reason for the error:
A space is required between the forcefield parameter code and the semicolon
indicating a comment, i.e.:
No default G96Bond types error:
3132 2gb_18; C-O ether bond <- line 88
Works fine:
3132 2
Hi,
Finally I found the reason for the error:
A space is required between the forcefield parameter code and the semicolon
indicating a comment, i.e.:
No default G96Bond types error:
>3132 2gb_18; C-O ether bond <- line 88
Works fine:
>3132 2gb_18 ; C-O ether bo
On Thu, Oct 22, 2009 at 05:17, Enemark Soeren wrote:
> Ahh, now I understand - sorry, Omer!
>
> No problem, glad to help.
>
>
> In fact, I have compared all three single hydrogen RDFs and they are
> identical and also relatively smooth. Since, however, with 3 times more data
> points (all thre
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