Hi, dear all:
What is the highest possible simulation temperature for lipid bilayer
systems. The main transition temperatures for DPPC and POPC are about 315K
and 270K, respectively. However, we have cholesterols in our systems.
I've gone through some literatures and found that people used 425K in
Hi, dear all (especially for David):
When reading the paper "Thermodynamics of hydrogen bonding in hydrophilic
and hydrophobic media" and its supplementary material and the code
"gmx_hbond.c" for the analysis of hydrogen bond, I got questions:
1. When calculating the autocorrelation function of the
Hi, all:
I tried to pull a specific DPPC, say, r3, out of a pre-equilibrated bilayer
into the water along the positive z axis. For the pull code parameters, I
used:
pull = umbrella
pull_geometry= distance
pull_vec1 = 0. 0. 1.
pull_dim= N N
Hi, all:
I got the initial structure of a DPPC bilayer from Dr. Karttunen's website,
use the parameters (hopefully) from their paper: Patra, Karttunen, Hyvönen,
Falck, Lindqvist, Vattulainen, Biophys. J. *84*, 3636-3645 (2003) to run for
100ns then replace some DPPC molecules with cholesterols, do
Hi, all:
I'm trying to embed cholesterol molecules into a DOPC bilayer in a coarse
grained model.
The force field and coordinates for a pure DOPC bilayer and for cholesterol
were obtained on the MARTINI's site. I randomly replace a DOPC molecule with
a cholesterol molecule and do the energy minimiz
Dear all:
I've got a DOPC/cholesterol system, and I want to get the MSD of the DOPCs
near cholesterols.
According to the literature, the overall movement of the each monolayer
should be removed prior to the MSD analysis of individual molecules, my
question is how should I do this?
Thank you in adva
Dear users:
1. I have a lipid bilayer of POPC with cholesterols. I'm trying to calculate
the MSD of the POPCs which is nearest to cholesterols. The nearest POPCs are
defined as those POPC whose C13 atoms to O6 atoms from cholesterol distances
are less than a certain cutoff. Is there a good way to d
Hi, GROMACS users:
I'm trying to calculate the lifetime distribution between pairs of vectors.
The problem can be simplified as: there are many vectors in any one frame of
a MD trajectory, and when one vector is within a cutoff distance with
another vector, and their angle is larger than a cutoff a
Hi, everyone:
I'm trying to get the force field for sphingomyelin by modifying the force
filed of DPPC from Dr. Peter Tieleman's website.
But for LJ pairs, there's no description for LC2--OA, N--LP2, N--LH1 and
OA--LH1 in the [pairs] section from lipid.itp. Where can I get the
parameters for these
Hello, everyone:
I have a system which is composed of a lipid bilayer and water layers upon
each monolayers.
Now the problem is that after the simulation, the lipid bilayer shift upward
inside the simulation box , and makes the upper water layer thinner, while
the lower water layer thicker.
In md
Hello, all:
I'm not sure how to make the .dat file in calculating the electron density,
for example,
If I have cholesterol.itp like:
; nrtype resnr residuatomcgnrcharge ; total charge
1 CH3 1CHOL C11 0
2 CB 1CHOL C2
Hi, all:I'm trying to run a simulation on DOPC bilayer, I've downloaded the pdb file of DOPC from Dr. Scott Feller's website. Currently my questions are:1. how to delete those hydrogens. When I use pdb2gmx, it complains residue "OLE" not found;
2. how to make the topology file, dopc.itp. I know the
Hi, everyone:I'm new in GROMACS. Currently I'm trying to build a lipid bilayer system with 40% POPC and 60% CHOLESTEROL, solvated in water. I got the 128 popc pdb file from Peter Tielemen's website. And in the literature I get that I should replace POPC with CHOL at some proper position in order to
13 matches
Mail list logo
