On 2/8/19 5:20 PM, James wrote:
Hi,
I know that gromacs has an hbond command which will analyze hbonds after a
run. But, during a run, without doing something like specifying partial
charges, do hbonds exist?
It seems to me that they do not, because if I put two water molecules next
to each
Hi,
I know that gromacs has an hbond command which will analyze hbonds after a
run. But, during a run, without doing something like specifying partial
charges, do hbonds exist?
It seems to me that they do not, because if I put two water molecules next
to each other, they do not assume the
Sorry, if the attachments don't load, here are the uploaded texts.
Thank you once again,
Angelina
*Job submission: *
#!/bin/bash
# Set some environment variables
FREE_ENERGY=`pwd`
echo "Free energy home directory set to $FREE_ENERGY"
MDP=$FREE_ENERGY/MDP
echo ".mdp files are stored in $MDP"
I am trying to calculate the free energy of curcumin in water. My system
goes from 0- 21 lambdas, but it is not recognizing my final lambda. I am
sure that I have 21 transitions for vdw_lambdas, coul_lambdas,
bounded_lambdas, resistant_lambdas, mass_lambdas, and temperature_lambdas.
I do not
Sir,
Can anyone suggest how I can use ethanol force field to solvate and run MD
for my molecule. Please help.
On Thu 31 Jan, 2019, 10:48 AM Satya Ranjan Sahoo Sir,
> I am a beginner to GROMACS. I was unable to understand how to create all
> the ions.mdp , md.mdp , mout.mdp , minim.mdp ,
any help please?
On Fri, Feb 8, 2019 at 12:39 PM Amin Rouy wrote:
> gmx tcaf
>
> http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-tcaf.html
>
> On Fri, Feb 8, 2019 at 11:48 AM Benson Muite wrote:
>
>> Which part of the manual does this refer to?
>>
>> On 2/8/19 12:42 PM, Amin Rouy
Hi,
http://manual.gromacs.org/documentation/current/user-guide/cmdline.html#command-changes-between-versions
help?
Em qua, 6 de fev de 2019 às 14:48, Antonio PEÓN escreveu:
> Hello,
>
> I would like to calculate the distance from the center of masses (COM)
> between two systems. One would be
On 2/8/19 9:36 AM, Edjan Silva wrote:
Dear users.
I can not execute the following command:
$ gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr
The error message that appears is:
-
Program:
Dear users.
I can not execute the following command:
$ gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr
The error message that appears is:
-
Program: gmx grompp, version 2019-beta3
Source
ok -- thanks -- am to trying this out now.btw, I am also running 2016.3
to analyze a trajectory made with 2016.4. I tried a couple of versions
and still got the same weird behavior, but I thought I'd let you know in
case you know that using a slightly older version to analyze a newer one is
...and molecules at the edges can totally be broken. So really just a
translation of the box coordinates to be centered on the desired group. It
should really be very straighforward.
If it's easier to take offline, I'm happy to.
M
On Fri, Feb 8, 2019 at 8:29 AM Mala L Radhakrishnan
wrote:
>
On 2/8/19 8:29 AM, Mala L Radhakrishnan wrote:
Hi Justin,
Yes, but I don't want anything sticking out of the box. I need the shape
of my entire system, when visualized, to be wholly contained within the
cubic shape -- and centered on the desired group. That's pretty much all.
Does this
Hi Justin,
Yes, but I don't want anything sticking out of the box. I need the shape
of my entire system, when visualized, to be wholly contained within the
cubic shape -- and centered on the desired group. That's pretty much all.
Does this clarify? Does this change what you recommend?
Mala
On 2/8/19 8:15 AM, Mala L Radhakrishnan wrote:
Hi Justin,
Also -- this is important, I need to maintain the shape of the cubic box,
so I do *not* want to keep molecules at the box edges whole (I know this
sounds weird, but I need it for my applications) -- so should I use -pbc
atom instead
Hi Justin,
Also -- this is important, I need to maintain the shape of the cubic box,
so I do *not* want to keep molecules at the box edges whole (I know this
sounds weird, but I need it for my applications) -- so should I use -pbc
atom instead of -pbc mol for the first step?
Thanks again so much
Hi Rajat,
Thanks -- but I don't want -pbc mol because that keeps my molecules whole,
which I don't want. I actually want to keep the shape of the cubic box for
my purposes. Maybe I'll try -pbc atom -ur compact, but I think I tried that
and it didn't work -- but will try again.
Mala
On Fri, Feb
On 2/8/19 8:03 AM, Mala L Radhakrishnan wrote:
Hi Justin,
Thank you SO much -- I will try this out, but I have a silly question
before I do -- is there a way to dump just the desired frame in the first
step itself -- or would that screw up the ordering -- since my xtc files
are just so huge
Hi Justin,
Thank you SO much -- I will try this out, but I have a silly question
before I do -- is there a way to dump just the desired frame in the first
step itself -- or would that screw up the ordering -- since my xtc files
are just so huge and I'd rather not create more huge files than
On 2/8/19 7:22 AM, Rajat Desikan wrote:
Hi Justin,
"A cubic box is already as compact as it can be."
That's true and I understand that :) it's just that I have faced similar
issues with trjconv that Mala appears to be grappling with, and this
combination has always resolves it for me. I don't
Hi Justin,
"A cubic box is already as compact as it can be."
That's true and I understand that :) it's just that I have faced similar
issues with trjconv that Mala appears to be grappling with, and this
combination has always resolves it for me. I don't know why. I can attach
test files that show
On 2/7/19 4:35 PM, Shujie Fan wrote:
Dear all,
I would like to run simulation for some small molecules containing
Chlorine with CHARMM36 forcefield. I was using cgenff to generate
the gromacs topologies. It seems cgenff_charmm2gmx.py script
currently cannot convert topologies containing
On 2/8/19 5:17 AM, Rajat Desikan wrote:
Hi Mala,
Please combine -center with "-pbc mol -ur compact" and check.
Compact unit cell representation is only useful for dodecahedral and
octahedral boxes. A cubic box is already as compact as it can be.
-Justin
--
On 2/8/19 6:52 AM, Mala L Radhakrishnan wrote:
Hi Paul,
Thanks for this idea --
...But it returns what I would expect:
Statistics over 1 steps [ 20. through 20. ps ], 3 data sets
All statistics are over 1 points
Energy Average Err.Est. RMSD
Hi Paul,
Thanks for this idea --
...But it returns what I would expect:
Statistics over 1 steps [ 20. through 20. ps ], 3 data sets
All statistics are over 1 points
Energy Average Err.Est. RMSD Tot-Drift
gmx tcaf
http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-tcaf.html
On Fri, Feb 8, 2019 at 11:48 AM Benson Muite wrote:
> Which part of the manual does this refer to?
>
> On 2/8/19 12:42 PM, Amin Rouy wrote:
> > Hi,
> >
> > I am sorry, but the manual is not clear to me. Does Tcaf
Which part of the manual does this refer to?
On 2/8/19 12:42 PM, Amin Rouy wrote:
> Hi,
>
> I am sorry, but the manual is not clear to me. Does Tcaf calculates the
> viscosity in all x,y,z directions?
> the manual says:
> Transverse currents are calculated using the k-vectors (1,0,0) and (2,0,0)
Hi,
I am sorry, but the manual is not clear to me. Does Tcaf calculates the
viscosity in all x,y,z directions?
the manual says:
Transverse currents are calculated using the k-vectors (1,0,0) and (2,0,0)
each also in the *y*- and *z*-direction
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What does "gmx energy -b 2 -e 2" give as box dimensions?
Peter
On 07-02-19 22:20, Mala L Radhakrishnan wrote:
> Hi Justin,
>
> Thank you -- the good news is that the center of mass of this group does in
> fact match what I calculate to be the COM with my script.
>
> BUT, the bad news is
Hi GROMACS users,
due to a recently discovered and fixed bug that caused unintended
behaviour of GROMACS that could result in wrong physical behaviour of
simulated systems, we decided to release one more point release of the
2016 branch of GROMACS, even though the branch has been official
Hi Mala,
Please combine -center with "-pbc mol -ur compact" and check.
Regards,
Rajat
--
Dr. Rajat Desikan
Invictus Oncology, Delhi
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