Hi,
I have a protein/lipid system.
Using charmm36 ff and gromacs5.1.4.
I set constraints = h-bonds because of charmm.
1. After that grompp complains about the oscillation between an O and H
in the lipid. Why? It should not.
Possible explanations I can imagine:
- does gromacs constrain only pro
Dear Gromacs developers,
Following is my email address for posting queries to GROMACS
srivastav...@iitj.ac.in
Best regards,
*Abhinav Srivastava*
*Research Scholar*
Indian Institute of Technology, Jodhpur
Rajasthan
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On Mon, 8 May 2017 13:44 Abhinav Srivastava (P14CHM002) <
srivastav...@iitj.ac.in> wrote:
> Dear Gromacs developers,
>
> Following is my email address for posting queries to GROMACS
> srivastav...@iitj.ac.in
>
> Best regards,
>
> *Ab
On 5/8/17 4:32 AM, Tamas Hegedus wrote:
Hi,
I have a protein/lipid system.
Using charmm36 ff and gromacs5.1.4.
I set constraints = h-bonds because of charmm.
1. After that grompp complains about the oscillation between an O and H in the
lipid. Why? It should not.
Possible explanations I can i
On 5/7/17 2:56 PM, Ali Shomali wrote:
Thanks so much Justin for your answer. actually I performed different
simulations and compared the area per lipid with existing studies . for
example I used gromacs charmm 22 for DPPC simulation and compared the
results with Dr.Feller's paper. also I conduc
On 5/7/17 2:22 PM, abhisek Mondal wrote:
Hello Justin,
Thank you for the explanation. I'm really new to the field so choosing
factors in a bit confusion.
You said in this set up the ligand can still move around X and Y direction.
My question is what if I set pull_k1=0? The ligand also won't mo
Good afternoon,
I’m trying to do molecular dynamics (protein-ligand) with a ligand that has a
boron atom.
Can anyone help me or give me some information how can I do the
parameterization of the ligand.
Best Regards,
Pedro Fernandes
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On Sun, May 7, 2017 at 11:37 PM, Justin Lemkul wrote:
>
>
> On 5/7/17 1:57 AM, abhisek Mondal wrote:
>
>> Hi,
>>
>> For your ease of understanding regarding what is happening during this
>> above said umbrella-mdrun, I have shared the trajectory video file the
>> following link.
>> https://drive.
Every time I ran through this step I needed to use -maxwarn. It raises no
issues later on.
On Fri, Apr 14, 2017 at 11:42 PM, Thomas Piggot
wrote:
> I too also fairly frequently use the -maxwarn option for this message.
> Perhaps it would be better off as a grompp note rather than a warning, or
>
On 5/8/17 9:04 AM, Pedro Fernandes wrote:
Good afternoon,
I’m trying to do molecular dynamics (protein-ligand) with a ligand that has a
boron atom.
Can anyone help me or give me some information how can I do the
parameterization of the ligand.
The details will depend on the force field yo
On 5/8/17 10:00 AM, abhisek Mondal wrote:
On Sun, May 7, 2017 at 11:37 PM, Justin Lemkul wrote:
On 5/7/17 1:57 AM, abhisek Mondal wrote:
Hi,
For your ease of understanding regarding what is happening during this
above said umbrella-mdrun, I have shared the trajectory video file the
foll
Hi gromacs user,
A peptide(p), a solid surface(s) in water(w) solution are the three
ingredients of my system. The total internal energy (Utot) of the system in
NVT ensemble, can be defined as Utot = Upp + Uww + Upw + Usw + Ups , where
the Uxy is the internal energy of interaction between x and y.
Dear users:
I have a bunch of trajectories of the same system. I want to cluster them
together (using gmx cluster gromos algorithm), identify the centroids, and then
use gmx rms to evaluate the RMSD to the centroid of the top N clusters in each
trajectory. The reason I want to do this is to be
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