Dear all,
I am a little bit confused about electrostatic force calculation
and need some clarification about PME.
I normaly use PME for electrostatic force
and rlist(=rcoulomb) is the parameter for real-space calculation.
As you know, rlist is related NS and nstlist (the neighbor list updat
Hi All,
I'm trying to run free energy simulations for a linkage change in an
oligosaccharide when bound to its protein.
The linkage changes from beta 1-4 to beta 1-3. I followed the tutorial by
Prof Mobley.
For the lambda values I took 0 to 1 at intervals of 0.05. The values of
dVpot/dlambda fro
rder= 6
ewald_rtol = 1e-4
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = no
Can anyone help me? Thank you in advance.
Thanks,
Shuangxing Dai
------ next part --
A
urierspacing will be used
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> ; EWALD/PME/PPPM parameters
> pme_order= 6
> ewald_rtol = 1e-4
> ewald_geometry = 3d
> epsilon_surface = 0
> o
This worked for me on AIX 5.3 for gromacs 4.0.4, I didn't try to
compile any gromacs versions after that because we found that gromacs
runs much better on Xeons and Opterons than it runs on power6's
running AIX 5.3
If you have a problem specific to 4.0.7 (i.e. you can compile 4.0.4
alrigh
Dear All,
I have problems with Compiling Gromacs 4.0.7 on AIX 5.3
using gromacs 4.0.7 and fftw 3.2.2
here is what I do for FFTW :
./configure --enable-float
make
make install
everything works fine
after that, I do some variable settings :
export CC='xlc_r'
export F77='xlf_r'
export FFL
My target system is a protein with lipid molecules added randomly (using
GENBOX). Running MD, I expect to have the protein "inserted" through
self-assembly. However, I encountered the crash every different trials. So I
broke down the problem, that is, to run md simulation for the protein
molecule o
I have been using g_wham, but I have a few questions that I can't find
answers to online. When using WHAM, one does not need the forces between
the pull groups to calculate the PMF, yet g_wham won't run without it. Is
there a reason for this?
I have never used g_wham, but g_wham -h (gromacs-4.
Hello,
On 15.04.2010, at 16:18, Mark Abraham wrote:
> On 16/04/2010 12:02 AM, Shuangxing Dai wrote:
>> Hi, gmx-users:
>>I am using latest version of gromacs and found it was really slow. I
>> was wondering anyone got the same experience and can point out where the
>> problem is.
>>I was
On 16/04/2010 12:02 AM, Shuangxing Dai wrote:
Hi, gmx-users:
I am using latest version of gromacs and found it was really slow. I
was wondering anyone got the same experience and can point out where the
problem is.
I was running double precision for MD. But for each dynamics
simulation, i
What makes you think it should be so fast?
Nothing appears obviously wrong in the mdp file.
May be this though!
lincs-order = 12
On Apr 15, 2010, at 4:02 PM, Shuangxing Dai wrote:
Hi, gmx-users:
I am using latest version of gromacs and found it was really
slow. I was wonde
Shuangxing Dai wrote:
Hi, gmx-users:
I am using latest version of gromacs and found it was really slow. I
was wondering anyone got the same experience and can point out where the
problem is.
I was running double precision for MD. But for each dynamics
simulation, it takes 4 days. I sh
Hi, gmx-users:
I am using latest version of gromacs and found it was really slow. I was
wondering anyone got the same experience and can point out where the problem
is.
I was running double precision for MD. But for each dynamics simulation,
it takes 4 days. I should only take two or three ho
Hi
I pulled an ion to move along the axial direction in a nanotube by using SMD
simulation, with the version of Gromacs-4.0.7. For some cases, the simulations
stopped without any errors. The simulation could properly run, but it did not
run to the end. The following is the pulling code in my .md
It is mot likely that your preparation of the system is somehow
corrupted.
The insertion of a protein in a lipid bilayer might easily introduce
strong
forces in the system and thereby result in a crash of your simulation.
It is also possible that your protein topology is not describing your
Hi all,
I have a system which is composed of hexane-peptide-water-peptide-hexane
layers. There, I selected the hexane+peptide system as the calculation
group, and the hexane group as the output group to calculate the hexane area
that is in contact with water. To do this I used the g_sas command wi
Dear gmx users,
I'm trying to run some CG-MD with gromacs, using the available Martini FF.
The first run with {lipid + water} is fine. The POPC lipid bilayer is
successfully self-assembled. I then applied Martini FF for system involving
protein.
All the systems I've tried so far could not survive a
Hi Par and Mark,
Thanks for the suggestions. You may be correct, using gromacs version
4.0.5 Charmm ff didn't worked straight away in my first attempt, but it
works after i made some modification here and there.
Best regards,
Rama
On Thu, Apr 15, 2010 at 2:47 AM, Pär Bjelkmar wrote:
> Hi,
>
Hi,
15 apr 2010 kl. 11.11 skrev Ramachandran G:
> Hello Par:
>Using the latest git i could able to work on my oxy-hemoglobin system
> with new gromacs version 4.0.5 successfully.
CHARMM is not supportd in version 4.0.5, you probably mean the developer
version?
> But since my new groma
for the position restrain simulations have a llok at :
http://www.gromacs.org/Documentation/How-tos/Position_Restraints
Starting from an homology model you should expect some relaxation
of the structure during the simulation.
On Apr 15, 2010, at 11:06 AM, sonali dhindwal wrote:
Thanks for the
On 15/04/2010 7:11 PM, Ramachandran G wrote:
Hello Par:
Using the latest git i could able to work on my oxy-hemoglobin
system with new gromacs version 4.0.5 successfully. But since my new
gromacs version was not installed in parallel i tried using older
version of gromacs 3.3.1 which was
Hello Par:
Using the latest git i could able to work on my oxy-hemoglobin
system with new gromacs version 4.0.5 successfully. But since my new gromacs
version was not installed in parallel i tried using older version of gromacs
3.3.1 which was installed in parrallel. While doing grompp to g
Thanks for the answer,
My protein strucutre is a homology model,,on which i want to do the simulation.
and the change in conformation after MD simulation is more than RMSD of 2
Angstrom, that too in the active site of the protein
and you said that "Using position restrain on the heavy atoms of t
There are gmx tools that explicitly do this. Either you determine which
lipid to remove using a visualization tool like VMD and remove the
lipids by editing the gro/pdb file, either you use on of the tools
associated
with gmx to insert a protein a membrane bilayer.
on the gmx tutorials:
http:
The distortion of a protein starting structure can result from various
reasons:
1- experimental determination of the structure: this include the
experimental
conditions (T, pH) as well as the crystal contacts if X-ray were used,
dynamics
of some part of the molecule if NMR.
2- the manner y
On Apr 15, 2010, at 3:05 AM, Sanku M wrote:
Hi,
I was interested in calculating the diffusion constant of the
center of mass of entire lipid-bilayer ( not individual lipid
molecules). Regarding this, I had two doubts I wanted to clarify:
1. Since I am interested in calculating the di
Hello,
Can anyone tell me how to remove overlapping lipid residues?
Thanking you.
--
Best Wishes,
Jignesh Patel
Pharmacoinformatics,
NIPER
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