dear teacher,
when i do remd in the npt ensemble.
=md.mdp===
; Start time and timestep in ps
tinit= 0
dt = 0.01
nsteps = 5000
; For exact run continuation or redoing part of a run
; Temperature coupling
Dear all
I'm studying a membrane protein. I've run equilibration with the follwing
parameters - reference temperature =323k
integrator = md ; leap-frog integrator
nsteps = 5 ; 2 * 5 = 100 ps
dt = 0.002 ; 2 fs
tcoupl = V-rescale ; modified Berendsen thermostat
The
There is something not quite right here.
I grompp a gro file created from a pdb file using pdb2gmx and run MD to do
a single point energy calculation.
I then grompp the original pdb file and run MD to do a single point energy
calculation.
The values of potential energy values are different by
Do you mean that you do constrained position simulations and want to
know how to process the force? If so, read about thermodynamic
integration (TI). I mostly work with US and position restraints, but
for absolute constraints I believe that you should take the average
force at each
It's more useful if you provide more information. What was the .pdb
file (can I download it from the pdb databank?) was there water? what
version of gromacs? was it compiled in double or single precision?
what were your mdp parameters?
-- original message --
There is something not quite
Hello all,
I'm wondering if it's possible to use tables to simulate a z-dependent 12-3
potential. I'd have the following function:
V(z) = C12/(z-z0)^12 - C3/(z-z0)^3
and I'm trying to construct a table to match. Any hints to get me started
would be greatly appreciated.
Thank you!
Olivia
--
On 2011-11-26 15:58, Olivia Waring wrote:
Hello all,
I'm wondering if it's possible to use tables to simulate a z-dependent
12-3 potential. I'd have the following function:
V(z) = C12/(z-z0)^12 - C3/(z-z0)^3
and I'm trying to construct a table to match. Any hints to get me
started would be
When people do this for lipid bilayers, they compute depth-dependent
diffusion profiles (often diffusion is computed separately for lateral
diffusion and diffusion along the bilayer normal). Sounds like you
might do something similar. I doubt that the standard gromacs tools
will do this
On Sat, Nov 26, 2011 at 11:17 PM, chris.ne...@utoronto.ca wrote:
When people do this for lipid bilayers, they compute depth-dependent
diffusion profiles (often diffusion is computed separately for lateral
diffusion and diffusion along the bilayer normal). Sounds like you might do
something
There was no water. Version 4.5.5. Single precision. This is what I ran:
pdb2gmx -f 1.pdb -p g1 -o g1
grompp -f 1.mdp -c g1.gro -o g1.tpr -p g1.top
mdrun -v -s g1.tpr -c ag1.gro -g g1.log -e g1.ene
Potential energy: 1.19780e+02 kJ/mol
grompp -f 1.mdp -c 1.pdb -o g1.tpr -p g1.top
mdrun -v -s
On 2011-11-26 16:38, Igor Druz wrote:
There was no water. Version 4.5.5. Single precision. This is what I ran:
pdb2gmx -f 1.pdb -p g1 -o g1
grompp -f 1.mdp -c g1.gro -o g1.tpr -p g1.top
mdrun -v -s g1.tpr -c ag1.gro -g g1.log -e g1.ene
Potential energy: 1.19780e+02 kJ/mol
grompp -f 1.mdp -c
There is rounding because of angstroms vs nanometers and both files
maintain 3 decimal places (see below).
The intention of pdb2gmx is not to get a .gro , but to get a .top or
.itp file.
I see your point, but I don't think it matters. If you really need
that precision, then I'd think
I already knew the reason. But I had to find this out hard way. Now facing
a dreading prospect of repeating tons of calculations! Hence the request
for the bad for the health sign. Btw, gromacs issues a lot of warnings,
but not this one :D
What a bright idea to switch from angstroms to
yes exactly thats what I am trying to do.. Thanks a lot for the suggestion
Ramya
On Sat, Nov 26, 2011 at 7:26 AM, chris.ne...@utoronto.ca wrote:
Do you mean that you do constrained position simulations and want to know
how to process the force? If so, read about thermodynamic integration
1. why repeat the calculations? If you're talking about simulations
then there is no need to repeat them due to this. You will get
different answers with the same starting coordinates if you simply
change the initial velocities. If you're talking about instantaneous
energy calculations
Dear Prof.
I have some problems about g_clustsize program and I didn't find my answer in
mailing list. Please help me.
I don't know what is the base of selection for -cut option?
In my system after doing g_clustsize, when I see nclust.xvg file, it looks like
all the atoms in the system were
On Sat, Nov 26, 2011 at 5:35 PM, chris.ne...@utoronto.ca wrote
1. why repeat the calculations? If you're talking about simulations then
there is no need to repeat them due to this. You will get different answers
with the same starting coordinates if you simply change the initial
velocities.
On 2011-11-26 19:07, Igor Druz wrote:
On Sat, Nov 26, 2011 at 5:35 PM, chris.ne...@utoronto.ca
mailto:chris.ne...@utoronto.ca wrote
1. why repeat the calculations? If you're talking about simulations
then there is no need to repeat them due to this. You will get
different answers
On 2011-11-26 18:55, mohammad agha wrote:
Dear Prof.
I have some problems about g_clustsize program and I didn't find my
answer in mailing list. Please help me.
I don't know what is the base of selection for -cut option?
In my system after doing g_clustsize, when I see nclust.xvg file, it
looks
On Sat, Nov 26, 2011 at 6:37 PM, David van der Spoel
sp...@xray.bmc.uu.sewrote:
On 2011-11-26 19:07, Igor Druz wrote:
On Sat, Nov 26, 2011 at 5:35 PM, chris.ne...@utoronto.ca
mailto:chris.neale@utoronto.**ca chris.ne...@utoronto.ca wrote
1. why repeat the calculations? If you're talking
On 2011-11-26 20:15, Igor Druz wrote:
On Sat, Nov 26, 2011 at 6:37 PM, David van der Spoel
sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote:
On 2011-11-26 19:07, Igor Druz wrote:
On Sat, Nov 26, 2011 at 5:35 PM, chris.ne...@utoronto.ca
mailto:chris.ne...@utoronto.ca
Thanks David! That helped a lot. I'm now trying to use the walls feature
with a user-defined potential. My mdp file is shown below:
title = Alkanethiol SAM MD
; Run parameters
integrator = md; leap-frog integrator
nsteps = 50; 2 * 50 = 1000 ps,
On 2011-11-26 21:01, Olivia Waring wrote:
Thanks David! That helped a lot. I'm now trying to use the walls feature
with a user-defined potential. My mdp file is shown below:
title = Alkanethiol SAM MD
; Run parameters
integrator = md; leap-frog integrator
nsteps
Dear All,
Is there a way to let GROMACS to calculate and write the total dipole moment
on-the-fly?
I realize that g_dipoles can be used to calculate the total dipole moment using
a stored trajectory. However, for a large system it is not very feasible to
write the trajectory at a frequency
On 27/11/2011 5:07 AM, Igor Druz wrote:
On Sat, Nov 26, 2011 at 5:35 PM, chris.ne...@utoronto.ca
mailto:chris.ne...@utoronto.ca wrote
1. why repeat the calculations? If you're talking about
simulations then there is no need to repeat them due to this. You
will get different answers
Alex Jemulin wrote:
Dear all
I'm studying a membrane protein. I've run equilibration with the
follwing parameters - reference temperature =323k
integrator = md ; leap-frog integrator
nsteps = 5 ; 2 * 5 = 100 ps
dt = 0.002 ; 2 fs
tcoupl = V-rescale ; modified Berendsen thermostat
The
Dear Prof. Spoel
Thank you very much for your reply, but I don't understand what I want!
In the g_clustsize there is only -cut = Largest distance (nm) to be
considered in a cluster between my questions and I don't know the base of
selection for -cut. I practice different numbers for -cut
Dear Prof.
I have a system consists of 500 surfactants + 61000 water beads + 500 ion in
martini force field into cubic box with 20.3*20.3*20.3 dimensions, May I know
the best quantity for -d option in editconf program to prevent from artificial
forces, please?
Best Regards
Sara
--
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