On 3/9/16 12:28 PM, gozde ergin wrote:
Dear all,
I would like to compute the osmotic pressure directly from all-atom MD
simulations of concentrated aqueous solutions.
The basic idea is to introduce “virtual” walls to represent the effect of ideal
semipermeable membranes, separating a high
Dear all,
I would like to compute the osmotic pressure directly from all-atom MD
simulations of concentrated aqueous solutions.
The basic idea is to introduce “virtual” walls to represent the effect of ideal
semipermeable membranes, separating a high concentration region from a pure
water
Dear gromacs users
I want to force the citrate to cross the channel using SMD, but when I run
the tutorial Umbrella Sampling for my system adapting the entries mdp for
gromacs-5.0.5 my results are staying bad!!
I want see citrato crossing the channel, and in the "generating
configurations" the
Hi,
I don't think the hessian calculation is parallelized. Try running in one core.
HTH,
Rui Rodrigues
De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Em Nome De Alexander
Alexander
I've recently installed OpenMPI 1.10.2 alongside GROMACS 5.1.2. I've read
all over the web about how to, but I'm having issues left and right. I've
finally gotten to a point where *gmx* works, but in an odd way. I'll try to
explain without too much detail.
Machine1=
CPU: 8-core AMD FX9590
GPU:
Thank you Justin for your help.
On Wednesday, March 9, 2016 6:38 PM, Justin Lemkul wrote:
On 3/9/16 1:42 AM, mohammad r wrote:
> Thank you Parham and Justin, Excuse me I have another question, in simulation
> of a water-peptide system, is it necessary to use QM/MM
Hi everyone, I'm doing a TI calculation for a molecule that's of interest to me
and the results after gmx bar processed the dhdl.xvg files aren't so good at
certain points so I want to add some lambda values around the problematic ones
and I was wondering if this means I have to do the entire
Hello,
I am working with a confined system with damped motion of molecules in the x
and y directions. Is there a workaround that would allow to calculate just the
axial velocity (vz) autocorrelation rather than the total velocity
autocorrelation?
Best regards,
Michelle
--
Gromacs Users
Dear Gromacs user,
I was wondering why no .mtx file as hessian file was produced in my gmx
mdrun?
I used below command to submit my mdrun job:
gmx mdrun -deffnm md -s md.tpr -mtx hessian.mtx -ntomp 4 -ntmpi 4
neither md.mtx nor hessian.mtx!?
Cheers,
Alex
--
Gromacs Users mailing list
*
On 3/9/16 6:00 PM, Alexander Alexander wrote:
Dear Gromacs user,
I was wondering why no .mtx file as hessian file was produced in my gmx
mdrun?
I used below command to submit my mdrun job:
gmx mdrun -deffnm md -s md.tpr -mtx hessian.mtx -ntomp 4 -ntmpi 4
neither md.mtx nor hessian.mtx!?
Right!
T.
On Mar 9, 2016 12:24 PM, "neha chaudhary"
wrote:
> Hi,
>
> So all I have to do is to extract different configurations from my already
> performed MD simulation. Then I have to prepare a new system using that
> configuration with the following parameters and
Thanks Tsjerk for replying,
I want to ask one more question that to start with new velocities, what
changes I have to make and in which .mdp file?
Best Regards,
*Neha*
Research Scholar,
Centre for Computational Biology and Bioinformatics,
School of Life Sciences,
Central University of Himachal
Hi Neha,
Set
continuation = no
gen_vel = yes
(check http://manual.gromacs.org/online/mdp_opt.html#vel)
Best,
Tsjerk
On Wed, Mar 9, 2016 at 11:16 AM, neha chaudhary
wrote:
> Thanks Tsjerk for replying,
>
> I want to ask one more question that to start with new
Hi Neha,
You can perform a simulation first, and then extract configurations, which
you simulate with new starting velocities. Alternatively, you can generate
a number of different starting structures using elastic-network modeling,
like with the ElNemo server. Mind to first energy minimize the
Dear Gromacs users
I am doing a very simple MD with a constant electric field of 1 V/nm
along the positive z-direction in a system containing only one Na+ ion,
starting from rest.
The ion is not coupled to the thermostat and it is placed in a box of 4
nm* 4nm * 16 nm, in the X,Y,and Z
Hi,
So all I have to do is to extract different configurations from my already
performed MD simulation. Then I have to prepare a new system using that
configuration with the following parameters and rerun the simulations:
continuation = no
gen_vel = yes
gen-seed = -1
Right?
Best Regards,
Hi,
I am running gmx msd and would like to import the value of the calculated
diffusion coefficient and error that is output in my linux terminal. I know
I can view the trajectory with grace or parse the file in a text editor for
its values, but I would just like end calculation. Is there a way I
Dear Gromacs Experts,
How can I get a plot of a bond length/ valence angle/ dihedral angle during
simulation
from *xtc and *.ndx files? I am pretty sure that it is possible, but with
g_angle
and g_bond I can get only the distribution.
By the way, when I use
g_angle -f npt-md2-cent.xtc -n
On 3/9/16 1:42 AM, mohammad r wrote:
Thank you Parham and Justin, Excuse me I have another question, in simulation
of a water-peptide system, is it necessary to use QM/MM simulation during the
entire process? Because I didn't see it in the tutorials. By the way I
generated the pdb file by
On 3/9/16 10:01 AM, Dawid das wrote:
Dear Gromacs Experts,
How can I get a plot of a bond length/ valence angle/ dihedral angle during
simulation
from *xtc and *.ndx files? I am pretty sure that it is possible, but with
g_angle
and g_bond I can get only the distribution.
Get the bond
2016-03-09 16:07 GMT+01:00 Justin Lemkul :
>
> You are. That's what -all is for:
>
> "Plot all angles separately in the averages file, in the order of
> appearance in the index file."
>
> Open up angaver.xvg and you will see the average, then the two individual
> time series.
On 3/9/16 10:11 AM, Dawid das wrote:
2016-03-09 16:07 GMT+01:00 Justin Lemkul :
You are. That's what -all is for:
"Plot all angles separately in the averages file, in the order of
appearance in the index file."
Open up angaver.xvg and you will see the average, then the
O'right, I found my mistake.
Now it works fine.
Thank you!
2016-03-09 16:11 GMT+01:00 Justin Lemkul :
>
>
> On 3/9/16 10:11 AM, Dawid das wrote:
>
>> 2016-03-09 16:07 GMT+01:00 Justin Lemkul :
>>
>>
>>> You are. That's what -all is for:
>>>
>>> "Plot all
Hi everyone,
I am working on PP/PME optimization. But I
found while PP ranks could be controlled by, say -dd 9 8 8, PME node
decomposition CANNOT be tuned.
For instance, below is the basic information
for optimization:
- Using a fourier
Hello there,
Can anyone tell me how can I start my MD simulations with different
starting structure (random seed) for my protein-ligand complex. Can I start
with different sets of coordinates and velocities? If yes, how?
Thanks,
*Neha*
Research Scholar,
Centre for Computational Biology and
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