Hi,
I am trying to simulate a protein with an iodide ion ligand. However, I
can't find the non-bonded force field parameters for iodide ion. Does
anybody have any suggestions or have the source of those parameters?
Thank you.
Best
Yunlong
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Thanks Mark for your comments.
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Thanks and Regards,
Bipin Singh
On Thu, May 28, 2015 at 9:05 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:
Hi,
On Thu, May 28, 2015 at 5:23 PM bipin singh bipinel...@gmail.com wrote:
Hi all,
I have calculated SASA for a
The most important question is whether you want to maximize per
simulation or aggregate ns/day. What you list is certainly a decent
configuration, but unless you want to maximize the single sim
performance, you could consider single-socket boxes. Xeons are a bit
expensive ($2.6 list price for a
Hi Justin,
I am sorry to miss your email and send to the mail list another one.
I understand that there are no official parameters but is there any
other source that I can look up?
Thank you.
Yunlong
On 5/27/15 4:37 PM, Justin Lemkul wrote:
On 5/27/15 4:32 PM, Yunlong Liu wrote:
Hi all,
On 5/28/15 1:12 PM, Yunlong Liu wrote:
Hi Justin,
I am sorry to miss your email and send to the mail list another one.
I understand that there are no official parameters but is there any other source
that I can look up?
Look at early papers by Beglov and Roux, in which they derived the
Dear all,
I tried to concatenate two trajectories using the comand
trjcat -f Trajectory_total.xtc md26_out.xtc -o Trajectory_total_full.xtc
The process ended normaly:
Reading frame 1 time 3000310.000
Summary of files and start times used:
FileStart time
Hi everyone,
I'm trying to use the pairs_nb directive in order to decouple charge and
VDW interactions of a small ligand in water but I'm running into problems
with the implementation and understanding the manual. I know I could be
using the couple-moltype and couple-intramol commands in my mdp
If you're after OPLS topologies for GROMACS then one way to derive them is
via Schrödinger's Maestro (free academics version is sufficient) and
Andrey Frolov's
ffconv script (http://frolov-pchem.wikispaces.com/ffconv.py). You can
create a force field represesentation of a molecule with the former
Hi,
Our group has done many studies using enzymes in organic solvents (with
different amounts of water) and we always used the GROMOS FF for the
proteins and compatible parameters for the solvents. We can find a review
of enzyme simulations in nonaqueous solvents here:
Dear all,
I want to calculate the persistence length of a triple helix. After
minimization and equilibration, I did MD simulation without position restraints
for atoms.
I read the second paragraph of gmx polystat, and understood that for one chain,
I can choose its backbone atoms as the index
On 5/27/15 10:00 PM, Vy Phan wrote:
Dear Justin,
I am so thankful for your reply.
I still do not know how I can build the topology for the [image: $\gamma$]
-Glu.
I want to use gromos force field 54a7. Could you give some more guideline?
Instead of being at the alpha position, the peptide
On 5/28/15 4:43 AM, Giannis Gl wrote:
Dear all,
I tried to concatenate two trajectories using the comand
trjcat -f Trajectory_total.xtc md26_out.xtc -o Trajectory_total_full.xtc
The process ended normaly:
Reading frame 1 time 3000310.000
Summary of files and start times used:
Thanks Justin and Kalev this brings me already much further. I tried
ffld_server and it works just fine. However, it is like a black box. I can’t
really find the documentation on how ffld_server gets the charges. Do you know
where to find the documentation?
Thanks
On May 28, 2015, at 2:22
Hi,
Thanks for the good description of the problem!
It does look like [ pairs_nb ] is incompletely supported in grompp - that's
what that error message says. I would speculate that this has never worked
since Berk introduced it in 2008, to replace an old implementation of
[pairs] type 3. This
Dear list,
I'm trying to use a tabulated non-bonded potential with GMX 5.0.4, and
was reading through the manual.
Under 7.3.10, coulombtype user it says More information is in the
printed manual.
Does anyone know where I could find this?
Also related, out of curiosity, why are the dispersion and
Hi all,
I have calculated SASA for a group amino acid residues using GMX versions
5.0.1 and 4.6.3 and noted that there is significant difference in the
calculated values, as can be seen in figure at the link below.
https://drive.google.com/file/d/0ByHdYJNF-aRrTEFtNDR5dEEyZlU/view?usp=sharing
I
On 5/27/15 10:23 PM, Vy Phan wrote:
Dear Gromas User,
I want to making disulfide bonds between protein and glutathion (GSH).
The topology for GSH I got from Produg serve.
Don't do this; the topology will be of very poor quality. See
http://pubs.acs.org/doi/abs/10.1021/ci100335w
Could
On 5/27/15 11:06 PM, Vy Phan wrote:
Dear Gromacs Users
I use the force field 54a7 for protein. Can I simulate the protein-ligand
complex with topology of ligand get from PRODRG server.
See my response to your glutathione question. Don't use PRODRG topologies
unless you correct all the
Hi,
On Thu, May 28, 2015 at 5:23 PM bipin singh bipinel...@gmail.com wrote:
Hi all,
I have calculated SASA for a group amino acid residues using GMX versions
5.0.1 and 4.6.3 and noted that there is significant difference in the
calculated values, as can be seen in figure at the link below.
On Fri, May 22, 2015 at 4:37 PM, Kutzner, Carsten ckut...@gwdg.de wrote:
On 22 May 2015, at 16:08, Albert mailmd2...@gmail.com wrote:
how about the following:
2 x Intel Xeon E52680V3,12 cores, 2.53.3 GHz
My guess is that two TITAN X will be more than enough to
balance the CPU compute
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