Is there a reason to switch water models? Gromacs supports both the
traditional TIP3P and the CHARMM TIP3P (TIPS3P).
Since you need to reinitialize velocities, it may not be a good idea to use
Nose-Hoover and Parinello-Rahman straight away. Furthermore, you need
to gen_vel=yes since gromacs
hello:
I've installed gromacs in my macbookPro with 10.8 OS system. I am
trying to import gromacs trajectory which contains 6000 frames. However,
the VMD always clashed
VMD(552,0xac879a28) malloc: *** mmap(size=831488) failed (error code=12)
*** error: can't allocate region
*** set a
Hello,
You might want to use TIPS3P (special CHARMM TIP3P) instead of regular TIP3P
because some researchers observed that regular TIP3P can impact the area per
lipid significantly when simulating CHARMM lipid bilayer (see reference below).
Concerning the CHARMM36 lipid force field in
Depending on the # of atoms, 6000 frames may exceed the amount of ram a 32bit
application can address (4GB). If you're having problems with the 64bit
version, you should probably ask the vmd-l list.
The only workaround other than that is trjconv -skip and make a trajectory
file that skips
On 10/15/2012 08:46 AM, Peter C. Lai wrote:
Depending on the # of atoms, 6000 frames may exceed the amount of ram a 32bit
application can address (4GB). If you're having problems with the 64bit
version, you should probably ask the vmd-l list.
The only workaround other than that is trjconv -skip
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
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
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
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
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 p...@uab.edu wrote:
Is there no [atomtypes] section in the top file?
On 2012-10-15 03:53:54PM +0800,
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.
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
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
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.
Thanks a lot!
De: Justin Lemkul jalem...@vt.edu
Para: Discussion list for GROMACS users gmx-users@gromacs.org
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!
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
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
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 jalem...@vt.edu wrote:
On 10/13/12 9:49 AM, Arman Mahboubi Soufiani wrote:
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
--
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
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
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 list
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) +
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
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
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
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.
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
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
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
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
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
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
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
Dear Justin,
Thank you very much from your time.
Best Regards
Sara
- Original Message -
From: Justin Lemkul jalem...@vt.edu
To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users
gmx-users@gromacs.org
Cc:
Sent: Monday, October 15, 2012 9:54 PM
Subject: Re: [gmx-users]
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
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
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