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.
Dear Gromacs Users,
There are easy to get membrane with 64 DPPC or 128 DPPC for all atoms
simulation or coarse grained simulation, but is it possible to get a membrane
with 512 lipids? If so, where?
We also tried to build a 512 lipids system manually.
First by means of VMD where we combined 4 128
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 apar
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 quite
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 num
t;
Today's Topics:
1. Re: 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: Ma
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: Orders o
incremented by one unit for
each residue, even if there are gaps in the sequence, 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
Ji
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
ubject: Re: [gmx-users] A theoretical question
To: Discussion list for GROMACS users
Message-ID: <77408b9e13230.4f4d4...@anu.edu.au>
Content-Type: text/plain; charset="us-ascii"
On 28/02/12, "Du Jiangfeng (BIOCH)" wrote:
> Dear GMX-users,
>
> In my impression
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 estimatio
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 cou
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 Justi
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
ess.
-Justin
--
Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
============
---
Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========
--
Message: 4
Date: Wed, 16 May 2012 08:11:49 -0400
From
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:
> Dear Justin,
>
> Based on your questions to my simulation, I posted here yesterday hopefully
> it was the correct way to reply in this foru
arently, I am confused with
> pull_k1>0 combined with pull_rate1=0. In my mdp, i set "none" 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
>
*.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
md_p
t;> > position moved a lot (3nm for instance.) As for the windows simulation,
>>> > I didn't apply constraint but only the internal constraint in the itp
>>> > file. I still don't understand why it have to do constraint? why not
>>> > give
ing away for the molecule,
>>> spring gets strechted -> wants to relax -> molecule follows spring (like
>>> that what happens in afm pulling)
>>>
>>>
>>> Am 22.05.2012 15:40, schriebgmx-users-requ...@gromacs.org:
>>>>> Hi Justi
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
C
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
.
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. Unfortunat
.
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. Unfortunat
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 ;
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
numbers, constant
$procon=9.494/15; ## the protein 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 yo
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,
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: I
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 is
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 Ca
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 exac
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