Dear Kieu Thu
Thanks for your comment about free energy. Unfortunately, I could not send a
email to Paissoni Cristina in the Gromacs Forum.
Could you give me email address of Paissoni Cristina? Finding a tool for
calculation MM/PBSA with Gromacs is very vital for me.
Best Regards
Kiana
--
Dear users,
I am investigating protein crystal packing artifacts by doing equilibrium
simulations starting from a crystal structure. I would like to know if the
relaxations i see are reproducible, in the sense that many simulations with
independent velocities give the same general result.
My plan
Hi All,
I have a few older membrane simulations for which the COM for the upper and
lower leaflets were not removed in the course of the simulations. These are
pretty long simulations exceeding 300 ns.
I have trouble with post-processing of the trajectory.
To remove the COM of the upper and lower l
Daer Justin
I studied your tutorial (Umbrella Sampling). It is very beneficial for me.
The system you considered was the dissociation of a single peptide from the
growing end of an protofibril.
You considered following parameters:
Chain_B: reference group for pulling.
Chain_A: group to which pu
On 11/9/13 12:48 AM, pratibha wrote:
Sorry for the previous mistake. Instead of 53a7, the force field which I
used was 53a6.
53A6 is known to under-stabilize helices, so if a helix did not appear in a
simulation using this force field, it is not definitive proof that the structure
does no
On 11/9/13 5:24 AM, rajat desikan wrote:
Hi All,
I have a few older membrane simulations for which the COM for the upper and
lower leaflets were not removed in the course of the simulations. These are
pretty long simulations exceeding 300 ns.
I have trouble with post-processing of the trajector
On 11/9/13 8:22 AM, shahab shariati wrote:
Daer Justin
I studied your tutorial (Umbrella Sampling). It is very beneficial for me.
The system you considered was the dissociation of a single peptide from the
growing end of an protofibril.
You considered following parameters:
Chain_B: referenc
On 11/8/13 2:27 PM, Williams Ernesto Miranda Delgado wrote:
Greetings
The discussion list had helped me about understanding what to do when I
want to calculate binding free energy using LIE after doing MD simulation
using PME.
Now I need your help about choosing the simulation box size for liga
On 11/8/13 3:32 PM, Williams Ernesto Miranda Delgado wrote:
Greetings again
If I use a salt concentration for neutralizing the protein-ligand complex
and run MD using PME, and the ligand is neutral, do I perform ligand MD
simulation without adding any salt concentration? It could be relevant fo
Dear Justin
Thanks for your explanation.
My system contains lipid bilayer + drug + water molecules.
I want to calculate Potential of mean force as a function of the distance
between the centers of mass of drug and the lipid bilayer.
Box vector along which the pulling is being conducted is Z.
1
On 11/9/13 9:38 AM, shahab shariati wrote:
Dear Justin
Thanks for your explanation.
My system contains lipid bilayer + drug + water molecules.
I want to calculate Potential of mean force as a function of the distance
between the centers of mass of drug and the lipid bilayer.
Box vector alon
Hi Justin,
1) I am doing all three. -type x, -type y, -lateral z (xy) ...(I am looking
at anisotropy in dynamics if any)
2) Yes, 192 phosphate beads is exact. I have 384 lipids in my system
(192/leaflet)
If you were to remove the COM motion of individual leaflets and extract the
MSD, what would yo
On 11/9/13 11:37 AM, rajat desikan wrote:
Hi Justin,
1) I am doing all three. -type x, -type y, -lateral z (xy) ...(I am looking
at anisotropy in dynamics if any)
2) Yes, 192 phosphate beads is exact. I have 384 lipids in my system
(192/leaflet)
If you were to remove the COM motion of individu
Hi Justin,
Thanks for your time. I think I will use g_traj to spit out the P8
coordinates from upperP8_center_pbcnojump.xtc and write my own little MSD
routine :)
On Sat, Nov 9, 2013 at 11:36 PM, Justin Lemkul wrote:
>
>
> On 11/9/13 11:37 AM, rajat desikan wrote:
>
>> Hi Justin,
>> 1) I am do
On Sat, Nov 9, 2013 at 9:36 AM, alex.bjorling wrote:
> Dear users,
>
> I am investigating protein crystal packing artifacts by doing equilibrium
> simulations starting from a crystal structure. I would like to know if the
> relaxations i see are reproducible, in the sense that many simulations wit
Hi Justin,
I take it that both the sets of parameters should produce identical
macroscopic quantities.
For the GPU, is this a decent .mdp?
cutoff-scheme= Verlet
vdwtype = switch
rlist= 1.2
;rlistlong = 1.4 NOT USED IN GPU...IS THI
On 11/9/13 4:16 PM, rajat desikan wrote:
Hi Justin,
I take it that both the sets of parameters should produce identical
macroscopic quantities.
For the GPU, is this a decent .mdp?
cutoff-scheme= Verlet
vdwtype = switch
rlist= 1.2
;rlistlong = 1.4
On Sat, 9 Nov 2013, Gianluca Interlandi wrote:
Just to chime in. Here is a that paper might be helpful in understanding
the role of cuoffs in the CHARMM force field:
AU STEINBACH, PJ
BROOKS, BR
AF STEINBACH, PJ
BROOKS, BR
TI NEW SPHERICAL-CUTOFF METHODS FOR LONG-RANGE FORCES IN MACROMOLE
On 11/9/13 9:51 PM, Gianluca Interlandi wrote:
On Sat, 9 Nov 2013, Gianluca Interlandi wrote:
Just to chime in. Here is a that paper might be helpful in understanding the
role of cuoffs in the CHARMM force field:
AU STEINBACH, PJ
BROOKS, BR
AF STEINBACH, PJ
BROOKS, BR
TI NEW SPHERICAL
Hi Szilard,
Thank you very much for your suggestions.
>Actually, I was jumping to conclusions too early, as you mentioned AMD
>"cluster", I assumed you must have 12-16-core Opteron CPUs. If you
>have an 8-core (desktop?) AMD CPU, than you may not need to run more
>than one rank per GPU.
Yes, we
Hi,
I used the command g_hbond to find h-bond between residues 115-118 and
water. Then I used g_analyze to find out the average and it gives the value
for the hbonds like this :-
std. dev.relative deviation of
standard -
Dear Justin and Mark Thank you for your Previous reply
Can i Use the Following Intel Compiler for grmacs 4.6.2 in
centos Linux OS ?
Intel® C++ Composer XE 2013 for Linux
it Includes Intel® C++ Compiler, Intel® Integrated Performance Primitives 7.1,
Intel® Math Kernel Li
22 matches
Mail list logo
