Thank you for the guidance. I shall browse through for other alternatives.
:)
On Mon, May 28, 2018 at 6:14 PM, Groenhof, Gerrit wrote:
> Hi,
>
> Unfortunately, for this to work
> you need to have both heme and protein in one topology.
>
> best,
>
> gerrit
>
> Tidings and a good day.
>
> Hi,
>
>
What exactly is the issue? It isn't clear what the problem is; the
fact it is having trouble with using the tng file format, or the
output in the cube file that is then loaded into vmd?
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences
The ATB generator does a reasonable job, but for some reason it gets
some things wrong. If you can look at that topology, identify the
problematic parts of it, see if that is consistent with the
forcefield, and then if not adjust the parameters. Particularly I
have found that some angles are way
Maybe you checked .xtc file
Velocity is in .trr file
Quyen V. Vu
Web frontend developer
On Mon, May 28, 2018, 18:42 Mark Abraham wrote:
> Hi,
>
> Only if you asked for velocity information to be written to the trajectory,
> with nstvout
>
> Mark
>
> On Mon, May 28, 2018 at 1:06 PM Atila Petros
for liquids use oplsaa
On Mon, May 28, 2018 at 12:23 PM, Atila Petrosian wrote:
> Hi all,
>
> I want to do md simulation of oil hydrocarbon?
>
> Is there appropriate force field for these hydrocarbons in gromacs?
>
> What I see in gromacs force fields only was related to aminoacids and
> nucleot
Hi all,
I want to do md simulation of oil hydrocarbon?
Is there appropriate force field for these hydrocarbons in gromacs?
What I see in gromacs force fields only was related to aminoacids and
nucleotides.
What is your suggestion for md simulation of oil hydrocarbon?
Best,
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Dear Mark and Justin,
My problem was solved using trr file.
Thanks for guidance.
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Hi,
An xtc file only contains positions. Your nstvout affects the trr file.
Notice how sharing your command line got you the answer you needed ;-)
Mark
On Mon, May 28, 2018, 18:12 Atila Petrosian
wrote:
> Dear Justin,
>
> In my last md simulation, I used
>
> nstxout = 1000
> nstvout = 1000
> n
Dear Justin,
In my last md simulation, I used
nstxout = 1000
nstvout = 1000
nstxtcout = 1000
nstenergy = 1000
nstlog = 1000
After your suggestion, I used gmx traj -f npt.xtc -s npt.tpr -ov veloc.xvg
-n index.ndx
veloc.xvg file is as follows:
---
On 5/28/18 11:49 AM, Atila Petrosian wrote:
Dear Mark,
Thanks for your answer.
"Only if you asked for velocity information to be written to the
trajectory, with nstvout"
Usually, I use the following lines in mdp files:
nstxout = 1000
nstvout = 1000
nstxtcout = 1000
nstenergy = 1000
n
Dear Mark,
Thanks for your answer.
"Only if you asked for velocity information to be written to the
trajectory, with nstvout"
Usually, I use the following lines in mdp files:
nstxout = 1000
nstvout = 1000
nstxtcout = 1000
nstenergy = 1000
nstlog = 1000
But, I get only position of atoms
Hi all,
I want to do md simulation of oil hydrocarbon?
Is there appropriate force field for these hydrocarbons in gromacs?
Is it possible with gromacs?
Best,
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Hi,
yeah i missed the charge group number. Thanks for reminding
Cheers,
Momin
Am 28.05.2018 um 16:59 schrieb Justin Lemkul:
On 5/28/18 10:34 AM, Momin Ahmad wrote:
Hello,
how many decimal digits are allowed in .rtp files for partial charges?
i got this error:
###
On 5/28/18 10:34 AM, Momin Ahmad wrote:
Hello,
how many decimal digits are allowed in .rtp files for partial charges?
i got this error:
##
Using the Uff4mof force field in directory ./uff4mof.ff
No file 'watermodels.dat' found, will not include a water
Hello,
how many decimal digits are allowed in .rtp files for partial charges?
i got this error:
##
Using the Uff4mof force field in directory ./uff4mof.ff
No file 'watermodels.dat' found, will not include a water model
Reading benzene.pdb...
Read 'BENZENE
Hello,
Can anyone provide me the topology for Adenosine Monophosphate Molecule
(AMP)for Gromacs (gromos54a7 forcefield).
Thanks
Nikita Bora
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Hi,
Unfortunately, for this to work
you need to have both heme and protein in one topology.
best,
gerrit
Tidings and a good day.
Hi,
I'm looking at a QM-MM/Gromacs optimization for a Heme-CYP system. How do I
take it forward. I've found one strategy using a dummy atom in linker.
However, th
Hi,
Only if you asked for velocity information to be written to the trajectory,
with nstvout
Mark
On Mon, May 28, 2018 at 1:06 PM Atila Petrosian
wrote:
> Dear gromacs users,
>
> I did md simulation. I need to velocity values for each atoms in time
> steps.
>
> Can I get this parameter from tr
Dear gromacs users,
I did md simulation. I need to velocity values for each atoms in time steps.
Can I get this parameter from trajectory file directly?
How to obtain that?
Thanks
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thank you so much for your reply.
On 5/28/18, Soham Sarkar wrote:
> use the latest .tpr formed after production run else try
>
> tpbconv -s dynamic.tpr -o dynamic_new.tpr
>
> On Mon, May 28, 2018 at 3:29 PM, SHAHEE ISLAM
> wrote:
>
>> thank you so much.
>> after deleting from -select its now wo
Tidings and a good day.
Hi,
I'm looking at a QM-MM/Gromacs optimization for a Heme-CYP system. How do I
take it forward. I've found one strategy using a dummy atom in linker.
However, there's a small issue in this route. How do we incorporate the
dummy if the link we are pursuing is between the p
use the latest .tpr formed after production run else try
tpbconv -s dynamic.tpr -o dynamic_new.tpr
On Mon, May 28, 2018 at 3:29 PM, SHAHEE ISLAM wrote:
> thank you so much.
> after deleting from -select its now working.but the fatal error is
> Molecule in topology has atom numbers below and ab
Hi,
g_dist does not take selection arguments so you cannot use -select or
anything that was an argument to it. You can either rely on the default
selections that all GROMACS tools make if there is no index file, or use
e.g. g_select to make an index file with the selections you want.
Note that gm
The command should be
g_dist -f md_0_1_noPBC.xtc -s dynamic.tpr -n index.ndx -o distave.xvg
Then select Chain_A and Chain_B as per the indexing number
On Mon, May 28, 2018 at 3:24 PM, SHAHEE ISLAM wrote:
> after deleting -select
> this error is coming
> Invalid command line argument:
> cog of gr
thank you so much.
after deleting from -select its now working.but the fatal error is
Molecule in topology has atom numbers below and above natoms (565).
You are probably trying to use a trajectory which does not match the
first 565 atoms of the run input file.
You can make a matching run input fil
after deleting -select
this error is coming
Invalid command line argument:
cog of group "Chain_A" plus cog of group "Chain_B"
On 5/28/18, Soham Sarkar wrote:
> Delete from -select.. previous are ok
>
> On Mon, 28 May 2018, 3:12 pm SHAHEE ISLAM, wrote:
>
>> hi,
>> to calculate the distance betwe
Delete from -select.. previous are ok
On Mon, 28 May 2018, 3:12 pm SHAHEE ISLAM, wrote:
> hi,
> to calculate the distance between the center of geometry of two
> proteins, i am using this command
> g_dist -f md_0_1_noPBC.xtc -s dynamic.tpr -n index.ndx -o distave.xvg
> -select 'cog of group "Cha
hi,
to calculate the distance between the center of geometry of two
proteins, i am using this command
g_dist -f md_0_1_noPBC.xtc -s dynamic.tpr -n index.ndx -o distave.xvg
-select 'cog of group "Chain_A" plus cog of group "Chain_B"'
Invalid command line argument:
-select
here in this index file the
Dear All,
I have a simulation box of dimension 8*6*4 nm3. The center
of the box is the center of the two center of masses of two ss-DNA. I want
to calculate the 2D distribution of the ions surround the strands in the
box. I chose Chain_A, Chain_B and ion as three groups, rather I am
Dear Gromacs users,
Does anyone know the meaning of "D Gsolv" when you plot the area.xvg (output of
g_sas)?
Any help will highly been appreciated.
Best,
C.
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Dear Cristina,
how did you call xmgrace? Did you supply the "-nxy" switch before
area.xvg or volume.xvg?
Regards,
Andras
On 05/28/2018 09:45 AM, Gonzalez Fernandez, Cristina wrote:
> Dear Gromacs users,
>
>
>
>
>
> I want to calculate the hydrophobic and hydrophilic area of a protein by
> usi
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Dear Gromacs users,
I want to calculate the hydrophobic and hydrophilic area of a protein by using
the g_sas command. I have used:
g_sas -f md.xtc -s md.tpr -o area.xvg -tv volume.xvg
However, looking at the area.xvg with xmgrace, I can only see the hydrophobic
area not the hydrophilic.
That's not my intention - someone seeking a topology would do well to a)
know the past research to inform their decisions, including whether to
repeat deliberately, and b) also ask them to share input files.
I was obviously joking, not to derail this thread. Besides, in
biomolecular fields, FF
Hi,
On Mon, May 28, 2018 at 9:17 AM Alex wrote:
> Mark, please don't be one of those people telling young researchers that
> everything has already been done. :)
>
That's not my intention - someone seeking a topology would do well to a)
know the past research to inform their decisions, includin
Mark, please don't be one of those people telling young researchers that
everything has already been done. :)
My postdoc (a fellow, actually -- with her own project & funding) is
reading all these horrible papers and, according to her, everything has
been done. Drives me nuts!
Alex
On 5/28
Hi,
I found a couple of papers doing MD on colchicine and tubulin in a few
minutes on Google - maybe you should start there and also check your work
will be novel :-)
Mark
On Sat, May 26, 2018 at 8:00 AM Harutyun Sahakyan
wrote:
> Hi all,
>
>
>
> I use gromacs for MD simulations, but use charm
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