concentration based on ions' concentration.
mol/ml
$a=$energy*$cal/$t/$R; ## $energy here is the binding energy calculated from
umbrella sampling (kcal/mol)
$k=$ln**$a;
$kd=1/$k *$procon * (10**9); ## Kd vs Ka; unit is μM here.
Thank you,
Jiangfeng.
On 10/1/12 4:36 AM, Du Jiangfeng (BIOCH) wrote
Dear Everyone,
I have two questions about the conversion of binding energy to binding
affinity.
I predicted the binding energy of a protein-membrane complex by umbrella
sampling (based on Justin's tutorial). After sampling, the binding energy
should be the substract of (min-max) PMF. I have
Dear All,
I encountered a very weird result after performing NVT simulation, all the
waters aligned in lines, and they look like crystal cells. How did it turn out
like this by temperature coupling? The following is the nvt.mdp parameters:
; NVT equilibration
define = -DPOSRES
.
Then, How should I figure out the problem?
Jiangfeng.
On 28/07/2012 12:58 AM, Du Jiangfeng (BIOCH) wrote:
Dear All,
I just configured the mdrun-gpu. When I tested mdrun-gpu by running
gromacs-gpubench-dhfr.tar.gz which is from gromacs website. Unfortunately, it
failed with segmentation
.
Then, How should I figure out the problem?
Jiangfeng.
On 28/07/2012 12:58 AM, Du Jiangfeng (BIOCH) wrote:
Dear All,
I just configured the mdrun-gpu. When I tested mdrun-gpu by running
gromacs-gpubench-dhfr.tar.gz which is from gromacs website. Unfortunately, it
failed with segmentation
Dear All,
I just configured the mdrun-gpu. When I tested mdrun-gpu by running
gromacs-gpubench-dhfr.tar.gz which is from gromacs website. Unfortunately, it
failed with segmentation fault. I don't think the system has any equilibrium
problem since it works fine in mdrun. I will appreciate a
, Jiangfeng. On 5/22/12 9:36 AM, Du Jiangfeng (BIOCH) wrote:
Dear Justin,
Based on your questions to my simulation, I posted here yesterday
hopefully
it was the correct way to reply in this forum.
You've still replied to the entire digest message (which I've cut out);
please
9:36 AM, Du Jiangfeng (BIOCH) wrote:
Dear Justin,
Based on your questions to my simulation, I posted here yesterday
hopefully
it was the correct way to reply in this forum.
You've still replied to the entire digest message (which I've cut out);
please
make sure to keep replies free
For your second problem: you have to create this file by writing the group
numbers, which inform the script to decide which two groups to be selected for
distance calculation.
If you made it, you first problem would probably be solved.
Good luck,
Jiangfeng.
Jiangfeng Du, PhD Student
On 5/16/12 4:08 AM, Du Jiangfeng (BIOCH) wrote:
Dear Sir/Madam,
I have performed umbrella pulling and umbrella sampling my protein from a
DOPC/DOPS membrane. Unfortunately, the results are really bad (Energy curve
suddenly turns to zero at the last 1 nm) and the histograph does not show any
, profile.xvg.
Thank you with regards,
Jiangfeng.
On 5/22/12 9:36 AM, Du Jiangfeng (BIOCH) wrote:
Dear Justin,
Based on your questions to my simulation, I posted here yesterday hopefully
it was the correct way to reply in this forum.
You've still replied to the entire digest message (which I've
to LINCS,
because if I use all-bonds, an error of 1099 constraints but degrees
of freedom is only1074 occurs. Actually, there is no any window with a
designed distance. Here I attach the histo.xvg, profile.xvg. Thank you
with regards, Jiangfeng. On 5/22/12 9:36 AM, Du Jiangfeng (BIOCH) wrote
*.mdp files.
Jiangfeng.
Jiangfeng Du, PhD Student
Cardiovascular Research Institute Maastricht
Department of Biochemistry
P.O. Box 616
Mobile: +31-681741859
FAX: +31-43-3884159
6200 MD Maastricht
The Netherlands
md_umbrella.mdp
Description: md_umbrella.mdp
...@vt.edu
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 5/16/12 4:08 AM, Du Jiangfeng (BIOCH) wrote:
Dear Sir/Madam,
I have performed umbrella pulling and umbrella sampling my protein from a
DOPC/DOPS membrane. Unfortunately, the results are really bad (Energy curve
suddenly
Dear Justin and gmx friends,
Sorry to bother you again, but I am really not sure what went wrong with the
umbrella sampling simulation, which I followed Justin's tutorial. The energy
curve increased from zero to the maximum but suddenly went down (no plateau). I
think the reason probably is my
Dear Sir/Madam,
I have performed umbrella pulling and umbrella sampling my protein from a
DOPC/DOPS membrane. Unfortunately, the results are really bad (Energy curve
suddenly turns to zero at the last 1 nm) and the histograph does not show any
overlap. Actually, I did it strictly based on
Dear Friends,
I am doing MD simulation to a coarse grained system by using martini force
field. According to Martini recommendation, the MD time step should be in 20-40
fs.
Since I selected 20 fs, the warning comes: estimated oscillational period is
less than 5 times of the time step.
I
Dear GMX-users,
How about the accuracy of the binding energy calculation by umbrella sampling
for a coarse gained system in which a protein domain binding to membrane?
Coarse gained force fields are less accurate if compared with atomistic ones
and too many values from it are given by
Dear GMX-users,
In my impression, a conventional simulation should be composed by: assemble
system -- energy minimization -- NVT and NPT equilibration -- MD simulation,
right? Now assume this procedure is correct, how about if there is no
equilibration, as long as we set the temperature and
: [gmx-users] A theoretical question
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 77408b9e13230.4f4d4...@anu.edu.au
Content-Type: text/plain; charset=us-ascii
On 28/02/12, Du Jiangfeng (BIOCH) j...@maastrichtuniversity.nl wrote:
Dear GMX-users,
In my impression
: Mass fraction (Steven Neumann)
2. Re: g_dist (Justin A. Lemkul)
3. Orders of the residues in gromacs (Du Jiangfeng (BIOCH))
4. Re: Orders of the residues in gromacs (Justin A. Lemkul)
5. g_dist (dina dusti)
6. Re: g_dist (Mark Abraham)
7. Re: Mass fraction (Mark Abraham)
8. Re
of the residues in gromacs (Du Jiangfeng (BIOCH))
4. Re: Orders of the residues in gromacs (Justin A. Lemkul)
5. g_dist (dina dusti)
6. Re: g_dist (Mark Abraham)
7. Re: Mass fraction (Mark Abraham)
8. Re: Orders of the residues in gromacs (Jianguo Li
, it always starts at 0 and
is granted to be unique for each residue.
Cheers,
Rui Rodrigues
De: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] Em Nome De Du
Jiangfeng (BIOCH) [j...@maastrichtuniversity.nl]
Enviado: sexta-feira, 3 de Fevereiro
Dear Friends,
I want to measure some data of a special residue, for instance TRP143, from my
MD result. But i encountered a problem.
The residue number 143 is ordered in .gro file, while it seems the residue
orders is random in gromacs. It points to another residue when I specify
residue
Hi gmx-users,
I am trying to a study of GLA domain simulation in membrane by using coarse
gained models. There is a problem coming from converting all-atom model to
coarse gained because GLA domain contains some unusual residues (10 glutamate
residues were modified by carboxylation) and also
Hi Guys,
I want to run a protein which contains some carboxylated residues into a
membrane. I have had to add a special residue into itp file since there is no
any description in normal itp for GLA residue. I admit some values I added for
GLA residue were ambiguous because I don't know the
Dear Everyone,
I am going to simulate the interaction of prothrombin's Gla domain with
membrane in martini force field. Here I encountered a problem: there are 10
modified GLUs in GLA domain. Martini force field can't recognize them. How
should I overcome this problem?
What I want to do now
Dear Gromacs Users,
I am still struggling with PS_PC system for quiet a long time. I want to
distribute some DPPS lipids (Negative changed) in one leaflet of DSPC (Neutral)
membrane, however, the PS lipids go to both leaflets after EM simulation. How
to restrict PS just in one side?
Mention:
Dear Gro-users,
We made a PSPC(PS:20%, PC: 80%) membrane system. We want all the PS In one
leaflet but every time after EM and MD, the PS lipids would scatter into both
leaflets. Anyone knows how to keep PS in one leaflet?
Any suggestion is appreciated,
Albert and Jiang.
Jiangfeng Du, PhD
Dear Gromacs Users,
It comes to me with million problems per day during I am using gromacs. :(
Maybe you are the right persons i should ask about coarse grained protein-lipid
simulation. Right now I have a system with a bilayer (DOPCs) and a protein
(Histone). After EM simulation, it worked
Dear Gro users,
We created an all-atom system with 512 DPPCs by the method which was suggested
by Justin (genconf -f 128.gro -o 512.gro -nbox 2 2 1) and a CG system with 512
DSPCs by using Martini self assembly tutorial. We do get nice bilayers, however
after minimization, the systems break
Dear All,
I require a CG database of POPC for coarse grained simulation. Can anyone give
some suggestions for where to find it or how to make it by myself?
PS: the structure file of POPC was from the Biocomputing, Department of
Biological Sciences, University of Calgary.
Thank you in advance.
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