Dear Dan,
As you can see in the images I sent to you, there is no error massage in
output files. The properties of the system such as pressure or temperature
is so high, that's why I've concluded that the system is crashed.
Sincerely,
Iman
On Wed, Aug 30, 2017 at 12:44 AM, Iman Ahmadabadi <
Hi,
I will download and install APBS and try again.
I have already tried pre-compiled version of g_mmpbsa from the link you
suggested.
Thanks
Best Regards,
*Neha*
Research Scholar,
Centre for Computational Biology and Bioinformatics,
School of Life Sciences,
Central University of Himachal
Hell,
Download APBS and install it then use the binary package of g_mmpbsa. or
see here:
Pre-compiled executable program
Pre-compiled program does not require any external library or GROMACS and
APBS package. These programs are standalone and without any dependency.
Download, extract and use
Hello,
I have not installed APBS. I have compiled g_mmpbsa without APBS. Should I
compile it with APBS?
Best Regards,
*Neha*
Research Scholar,
Centre for Computational Biology and Bioinformatics,
School of Life Sciences,
Central University of Himachal Pradesh,
On Wed, Aug 30, 2017 at
Hi,
The segmentation fault error during polar energy calculations is due to
APBS. I don't know whether you installed it properly or not.
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Hi, gmx users,
I am wondering how can I set up a pure repulsive or attractive LJ potential
in the OPLSAA force field. Since you need to set up the sigma and epsilon
instead of C6 or C12, the pure repulsive requires sigma to be infinity and
epsilon need to be 0. Is there a way to achieve pure
Iman,
You get the error message in the terminal if you are running it on your own
machine. If you are running on a supercomputer, the error messages will be
directed to a file. How do you know the simulation is crashing without the
software telling you? Please find the message (check all
Hi Dan,
There is no error massage, It's just a crashing and stopping the
simulation. The version is 4.6.0.
Iman
On Tue, Aug 29, 2017 at 9:57 PM, Iman Ahmadabadi wrote:
> Dear Dan,
>
> I have attached the NPT.mdp file in the following:
>
> title = NPT
Hi, Dan,
Thanks for your response. The interfacial tensions I get from gmx energy
is way larger than the typical surface free energy of solid. So I suspect
the freeze command may have generated some artifacts and I need to find a
better force field.
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Dear Dan,
I have attached the NPT.mdp file in the following:
title = NPT equilibration
; Run parameters
integrator = md
nsteps = 2000
dt= 0.001
; Output control
nstxout = 500
nstvout = 500
nstenergy = 500
nstlog = 500
; Bond parameters
continuation= no
constraint_algorithm
Hi All,
Am just wondering if somebody has seen this in different gmx versions?
Thanks.
JIom
On Fri, Aug 25, 2017 at 11:00 AM, gromacs query
wrote:
> Hi All,
>
> I am using 'equivalent' mdp settings for pull run in Gromacs 4.6 and 2016.
>
> With gromacs 4.6 I get time,
Hi Lei,
1. In the Gromacs manual you can find the formula that the software uses to
calculate surface tension. It is just based on a few components of the
pressure tensor, so I imagine you can just use gmx energy (or g_energy
depending on the version of Gromacs you are using).
2. Freezing doesn't
What is the error message?
What version of Gromacs are you using?
Can you post the entire .mdp file?
On Tue, Aug 29, 2017 at 9:34 AM, Iman Ahmadabadi wrote:
> Dear All Users,
>
> I'm calculating the surface tension of the water, my box contains almost
> 5000 water
Dear All Users,
I'm calculating the surface tension of the water, my box contains almost
5000 water molecule in the middle of that. Through NVT equilibration, I got
reasonable results for surface tension but when I use NPT for my system,
the system crashes every time. The pressure coupling
Dear Eric and other Gromacs users,
Thanks for clarifying about how different timescale of trajectories can
affect lifetimes
But the case with and without pbc have same length of trajectories (100 ns).
Then why the difference in lifetimes ( 1793ps with pbc and 2345 without pbc)
Which can be
Thank you!
But still I do not understand what those values represents since there
isn´t a legend in the gmx analyze output. I understood that those 3 values
should be the average hbond lifetime, and the 2 constant k and k´. Am I
correct ?
The fitting is bad since I used long simulation time
Dear Apramita,
Right. Still, the same still applies with regards to the -666.
It could be a matter of statistics, why you get sensible values for the longer
trajectory chunk. Also, note that the trajectory length limits the possible
timescales that the model can tease out. If I understand
Dear Eric,
Its actually the DG(kj/mol) value which is -666. The time is coming to
be-126 ps. But the g_hbond is failing to fit the kinetic model to the data
for the last 60ns as you have implied. Any reasons why this could have
happened, while for the entire trajectory, I am getting positive
Dear Valerio,
Have a glance at the paper by Luzar and Chandler.
Btw: your data doesn’t fit with the kinetic model very well, hence the -666 for
the integral.
Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of
Dear all,
I am trying to obtain parameters for h-bonds. I used the tool gmx hbonds
with -ac option but resulted in segmentation fault. Therefore from the
normal gmx hbond output I used gmx analyze to obtain the autocorrelation
function. Therefore, using again gmx analyze with -luzar options and
Installing version 2016.3 worked perfectly. Thanks!
Regards,
Rajat
On Mon, Aug 28, 2017 at 12:08 PM, Vytautas Rakeviius wrote:
> You have updated boost so you have to update GROMACS too. 2016.3 is the
> latest version you should download it.
> Another possibility is to
On 8/29/17 12:09 AM, Neha Gupta wrote:
Hi Vytautas,
Thank you for your response..
I did as you told and got this message at the command prompt
libfftw3f: /usr/local/lib/libfftw3f.la /usr/local/lib/libfftw3f.a
But the error tells me :
gmx: error while loading shared libraries:
On 8/29/17 1:47 AM, Simon Kit Sang Chu wrote:
Dear every user,
I am using Andersen thermostat and nstcomm should be set to 1 (step).
However, after specifying nstcomm = 1, an error has returned -
nstcalenergy cannot be smaller than nstcomm. GROMACS automatically sets it
to nstcalenergy step.
Hi,
Firstly, you should confirm your gromacs version, gromacs 5.x certainly
includes nstcalenergy options in .mdp file. So you must set nstcalenergy=1
while the default value is 10 in .mdp if you want to nstcomm=1.
thanks
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Hello,
In the command to calculate rdf,
gmx rdf -f md.trr -s md.tpr -n abc.ndx -o rdf_abc.xvg -cn cn_abc.xvg
Is the cumulative number obtained using the -cn flag with gmx_rdf same as
coordination number?
If not, then how can I calculate coordination number from cumulative
number? or how can i
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