I'm getting control over my .mdp files, cutting down on the generation of
data for which I currently have no use. I just changed the nstenergy
parameter to 2500 cycles, much larger than its default value of 100 cycles.
This reduced logging still gives me plenty of data for monitoring the
stabilit
Not answering your main question here, just pointing out that you should try:
trjconv -pbc mol -ur compact
and then visualize with VMD to see if you are actually getting what you want
after all.
Chris.
-- original message --
I already pack the mixed solvent by using packmol cause the box that
Dear Justin,
Thank you very much from your time.
Best Regards
Sara
- Original Message -
From: Justin Lemkul
To: mohammad agha ; Discussion list for GROMACS users
Cc:
Sent: Monday, October 15, 2012 9:54 PM
Subject: Re: [gmx-users] about equilibrium
I didn't see anything inherently
On 10/15/12 1:03 PM, Amir Abbasi wrote:
tnx But I need these two planes angle too.
what should I do?
can I convert all of trajectory file to pdb?
in order to do these manually?
That would be extremely inefficient. Determining what's wrong with your index
file is probably a much better solu
I didn't see anything inherently wrong with your previous observations, so I
suspect your new approach is probably fine. There are several ways to do just
about anything; you just need to find one that works to your satisfaction and
represents a reasonable model of whatever you're trying to s
Dear Justin,
The previous problems was as is following:
> Dear GROMACS Users,
>
> I asked this question before but I don't understand it!
>
>
>
I placed several materials in my box of simulation for example box with
6nm*6nm*6nm and my materials are not placed in the smaller box but when
I equi
On 10/15/12 12:11 PM, mohammad agha wrote:
Dear Justin,
Thank you very much from your response. This question was because of my previous problems
about equilibration the box that I sent it with subject "equilibrium for box of
simulation". When I equilibrate solvent and additives separated
On 10/15/12 11:48 AM, Amir Abbasi wrote:
Hi !
I want to use g_sgangle to find distance between two groups (each group
includes 3 atoms).
I use this command:
g_sgangle -s md_1.tpr -f md_1_noPBC.xtc -n index.ndx -oa 12_angle.xvg -od
12_dist.xvg
but i got this error
Fatal error:
Error: no groups
On 10/15/12 11:45 AM, benjfitz wrote:
As a further check I ran a neat solvent box and the simulation ends abruptly
at 1.07 us.
These results suggest that your physical model is unstable. A linear model of a
triatomic species is not stable. A more appropriate approach is to use virtual
s
Dear Justin,
Thank you very much from your response. This question was because of my
previous problems about equilibration the box that I sent it with subject
"equilibrium for box of simulation". When I equilibrate solvent and additives
separated and then add to surfactant and after that equi
On 10/15/12 10:12 AM, Rajiv Gandhi wrote:
Dear Gromacs.
In experimental it says that the number of water molecule present in dimer
interface could be varied upon time of ligation process. I want to
calculate the number of water molecules in the protein dimer interface
during the simulation. Co
Hi !
I want to use g_sgangle to find distance between two groups (each group
includes 3 atoms).
I use this command:
g_sgangle -s md_1.tpr -f md_1_noPBC.xtc -n index.ndx -oa 12_angle.xvg -od
12_dist.xvg
but i got this error
Fatal error:
Error: no groups in indexfile
my index file:
[ G3 ]
76 8
As a further check I ran a neat solvent box and the simulation ends abruptly
at 1.07 us.
--
View this message in context:
http://gromacs.5086.n6.nabble.com/Diatomic-in-MeCN-NPT-NH-and-PR-simulation-segfaults-after-1-us-tp5001845p5002046.html
Sent from the GROMACS Users Forum mailing list archi
On 2012-10-15 16:53, Peter C. Lai wrote:
Isn't Mark's script outdated for this purpose?
I just uploaded a new script that seems to work:
http://www.gromacs.org/@api/deki/files/185/=charmm2gromacs-pvm.py
Please check the comment on
http://www.gromacs.org/Downloads/User_contributions/Other_sof
Isn't Mark's script outdated for this purpose?
charmm forcefields specify epsilon and sigmas so you only need to convert
them:
gromacs(sigma) = (charmm(Rmin/2)/10) * (2/(2^(1/6)))
gromacs(epsilon) = charmm(eps) * 4.184
For 1-4 pair interactions,
gromacs(sigma1,4 i,j) = (charmm(Rmin/2_1,4_i) + c
Hello,
I am calculating the dipole moment auto-correlation function for my system
which have 128 cation and 128 anion.
Due to the PBC, the function of the total dipole moment in time is not
continuous.
Can I removed PBC for g_dipole?
Thanks
Nilesh
--
gmx-users mailing listgmx-users@gr
Hello, everyone.
I used the Mark's script's to convert the CGenff (version 2b7 ) parameter
file to Gromacs .itp files. In the ffcharmmnb.itp, the script gave the c6
and c12, while the charmm's ffnonbond.itp showed epsilon and sigma.I do not
understand the relation between the c6/c12 and epsilon
On 10/15/12 8:56 AM, mohammad agha wrote:
Dear Gromacs Users,
I have one system consists of: surfactant, solvent and additives. I made one
box with only solvent and one box with only additives and equilibrated them
little separable for better placing into the box, and then made one box w
On 10/15/12 9:04 AM, Ali Alizadeh wrote:
Dear All users
I want to specify this statement in my input files but Where does it
specify?( i don't know!)
I know but i do not certain,
Force calculations were truncated at a distance of 1.2 nm
That likely refers to cutoff values.
-Justin
--
===
Dear Justin,
Thank you for your help, however, the problem was originated from absence
of -table table_d1.xvg flag in my mdrun command.
Now it is fixed.
BR
Arman
On Sat, Oct 13, 2012 at 10:30 PM, Justin Lemkul wrote:
>
>
> On 10/13/12 9:49 AM, Arman Mahboubi Soufiani wrote:
>
>> Dear Justin,
Hi Justin,
My original intention was to lessen the 5 ns trajectory to transfer to another
drive. I did
trjconv -f traj.trr -o traj_1.trr -b 0 -e 4000
When I saw the resulting file greatly lessened in size, that's when I tried as
a test
trjconv -f traj.trr -o traj_1.trr
I knew that it was not
Dear Gromacs Users,
I have one system consists of: surfactant, solvent and additives. I made one
box with only solvent and one box with only additives and equilibrated them
little separable for better placing into the box, and then made one box with
surfactant and then placed box of solvent
Thanks a lot!
De: Justin Lemkul
Para: Discussion list for GROMACS users
Enviadas: Segunda-feira, 15 de Outubro de 2012 9:42
Assunto: Re: [gmx-users] bonds braking
On 10/15/12 8:40 AM, Eduardo Oliveira wrote:
> Thanks!
>
> So, if i understood correctly the
On 10/15/12 8:40 AM, Eduardo Oliveira wrote:
Thanks!
So, if i understood correctly the correct workflow of trjconf?
I posted the link for two reasons: (1) so you would understand the nature of
what was actually happening in the simulation and (2) so you would be aware of
the solution. In
On 10/15/12 8:09 AM, Eduardo Oliveira wrote:
Hi,
I'm having trouble simulating a protein kinase on water. During the simulation,
the molecule moves towards the box limits and some residues apear on the other
side. Almost like they are interacting with water molecules on different sides
of t
Hi,
I'm having trouble simulating a protein kinase on water. During the simulation,
the molecule moves towards the box limits and some residues apear on the other
side. Almost like they are interacting with water molecules on different sides
of the box. I'm on my third simulation and the proble
On 10/15/12 7:50 AM, Gil Claudio wrote:
Hi Peter,
Same machine, all single precision.
Run gmxcheck -f -f2 on the two trajectories to see what's going on. Can you
explain what you were trying to do? I see no point in the trjconv command you
ran. Were there other flags that you haven't s
Hi Peter,
Same machine, all single precision.
Gil Claudio
On Oct 15, 2012, at 5:39 PM, "Peter C. Lai" wrote:
> Was traj.trr output by the same machine/mdrun as the machine you are running
> trjconv on?
>
> Is traj.trr (or the mdrun that wrote it) double precision and trjconv is
> compiled fl
On 2012-10-15 05:54:58AM -0400, Justin Lemkul wrote:
>
>
> On 10/15/12 5:45 AM, cuong nguyen wrote:
> > Dear,
> >
> > The top file downloaded from PRODRG did not consist of [atomtypes]. Please
> > tell me how can I add and use this function?
> >
>
> I see no need to change anything about the L-J
On 10/15/12 5:45 AM, cuong nguyen wrote:
Dear,
The top file downloaded from PRODRG did not consist of [atomtypes]. Please
tell me how can I add and use this function?
I see no need to change anything about the L-J parameters. Is there some reason
you believe them to be incorrect? If you
On 10/14/12 10:41 PM, Nur Syafiqah Abdul Ghani wrote:
Dear All,
I would like to do the simulation between water and other solvent.
One question that i curious to know which is how i want to put the
amount of solvent, HFIP before i insert the water?
Its suppose 80% of HFIP and 20% of water.
But
Dear,
The top file downloaded from PRODRG did not consist of [atomtypes]. Please
tell me how can I add and use this function?
Best regards,
Cuong
On 15 October 2012 16:43, Peter C. Lai wrote:
> Is there no [atomtypes] section in the top file?
>
> On 2012-10-15 03:53:54PM +0800, cuong nguyen w
Hi Jernej,
The CHARMM force field was developed for use with the TIP3P model making
this probably the appropriate choice, even if this model may not perform
the best for simulations of pure water (see
http://pubs.acs.org/doi/abs/10.1021/jz200167q for some more details).
As for some specific
Was traj.trr output by the same machine/mdrun as the machine you are running
trjconv on?
Is traj.trr (or the mdrun that wrote it) double precision and trjconv is
compiled float (single precision)?
On 2012-10-15 02:31:00AM -0700, Gil Claudio wrote:
> Hi all,
>
> When I do the following command
>
Hi all,
When I do the following command
trjconv -f traj.trr -o traj_1.trr
the file size of traj_1.trr is around 25% smaller than traj.trr.
Does traj_1.trr contain less data than traj.trr?
Thanks
Gil
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/
Is there no [atomtypes] section in the top file?
On 2012-10-15 03:53:54PM +0800, cuong nguyen wrote:
> Thanks for you email.
> I already had the .gro and .top files from PRODRG. Now I want to reproduce
> these files following the LJ parameters in a published paper (charge, sigma
> and epsilon valu
Thanks for you email.
I already had the .gro and .top files from PRODRG. Now I want to reproduce
these files following the LJ parameters in a published paper (charge, sigma
and epsilon values). I can change the charge in the top file, yet I do not
know how to change sigma and epsilon values.
Best
On 2012-10-15 03:10:18PM +0800, Jernej Zidar wrote:
> The reason for using SPCE instead of TIP3P is that it performs way
> better than TIP3P. This point is being emphasized everywhere along the
> documentation. I will try simulating using TIP3P model.
> >
> > Is there a reason to switch water mode
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