Hi,
Anybody knows where can I get the charmm36 parameters for POPG?
I couldn't find it in lipidbook. Has it been produced by any users?
Thanks in advance.
Sincerely,
Shima
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search
Hi,
I have a system of Peptide-popc-ions-water to simulate. I'm trying to run MD
simulation following the Justin's tutorial of kalp15-DPPC.
The force field which I use, is charmm36.
In NVT step, I get LINCS-warning as follow:
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation
On 1/1/13 8:56 AM, Shima Arasteh wrote:
Hi,
I have a system of Peptide-popc-ions-water to simulate. I'm trying to run MD
simulation following the Justin's tutorial of kalp15-DPPC.
The force field which I use, is charmm36.
In NVT step, I get LINCS-warning as follow:
Step 0, time 0 (ps)
Thanks.
I compared settings of mdp files in POPC/WATER and POPC/PROTEIN/WATER systems.
The only difference I found between them was about the bonds constraints. The
constraints of mdp file for POPC/WATER was constraints = h-bonds , however
it was constraints = all-bonds for POPC/PROTEIN/WATER
On 1/1/13 10:41 AM, Shima Arasteh wrote:
Thanks.
I compared settings of mdp files in POPC/WATER and POPC/PROTEIN/WATER systems. The only difference
I found between them was about the bonds constraints. The constraints of mdp file for POPC/WATER
was constraints = h-bonds , however it was
I used genconf and got a new gro file. Then I saw the ions are not recognized
because of the same numbering of ions with last SOL molecules. Therefore, I
changed them manually, so the problem was solved.
Thanks for your suggestions dear Justin.
Happy New Year!
Sincerely,
Shima
-
If I tell you that I changed the constraints and now the NVT is running, would
that be ok? However I don't know the scientific reason of this incident!
But I bring you the EM.mdp as follow:
define = -DSTRONG_POSRES
integrator = steep ; Algorithm (steep = steepest descent
On 1/1/13 10:53 AM, Shima Arasteh wrote:
If I tell you that I changed the constraints and now the NVT is running,
would that be ok? However I don't know the scientific reason of this incident!
But I bring you the EM.mdp as follow:
define = -DSTRONG_POSRES
integrator= steep
Thanks.
Sincerely,
Shima
- Original Message -
From: Justin Lemkul jalem...@vt.edu
To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS
users gmx-users@gromacs.org
Cc:
Sent: Tuesday, January 1, 2013 7:27 PM
Subject: Re: [gmx-users] LINCS WARNING -
Dear all,
Im trying to run an md or em using an implicit solvation method using
gromacs 4.5.5 but I allways get the same errors.
GB parameter(s) missing or negative for atom type 'OS'
GB parameter(s) missing or negative for atom type 'H2'
GB parameter(s) missing or negative for atom type
On 1/1/13 1:31 PM, Gert Peters wrote:
Dear all,
Im trying to run an md or em using an implicit solvation method using gromacs
4.5.5 but I allways get the same errors.
GB parameter(s) missing or negative for atom type 'OS'
GB parameter(s) missing or negative for atom type 'H2'
GB
Have someone else any ideas how the topology for a simple 2D lattice
could be done ?:)
I've tried to build it manually but for the system of 48 nodes
definition of the angles and impropers have appeared very routinely :(
James
2012/12/30, James Starlight jmsstarli...@gmail.com:
Hi Leandro!
On 1/1/13 2:06 PM, Parisa Rahmani wrote:
Hi gmx users
I want to do secondary structure analyze for my trajectory of protein.
I've downloaded DSSP packages from
ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4.tgz;
and put it in /usr/local/bin , and rename the folder to dssp.
when i run
On 1/1/13 2:01 PM, James Starlight wrote:
Have someone else any ideas how the topology for a simple 2D lattice
could be done ?:)
I've tried to build it manually but for the system of 48 nodes
definition of the angles and impropers have appeared very routinely :(
For regularly spaced atoms,
Thanks Justin for the reply,
how i can sure that it uses the DSSP package correctly ,
it seems that it just uses the gromacs code :
(
Opening library file /home/parisa/parisa/share/gromacs/top/phbres.dat
Opening library file /home/parisa/parisa/share/gromacs/top/aminoacids.dat
Opening library file
On 1/1/13 2:17 PM, Parisa Rahmani wrote:
Thanks Justin for the reply,
how i can sure that it uses the DSSP package correctly ,
it seems that it just uses the gromacs code :
(
Opening library file /home/parisa/parisa/share/gromacs/top/phbres.dat
Opening library file
Justin Lemkul wrote
On 1/1/13 1:31 PM, Gert Peters wrote:
Anyone got a clue? I dont think I did something wrong as the implicit
solvation
model previously worked. All input is appreciated.
From the path you've written above, it seems to imply you are modifying
the
gbsa.itp file in the
Dear advanced gromac users,
I am trying to simulate a long linear chain of polymer using CG beads. (about
200 beads), all with same type charge interactions. (examples shown:) I read on
previous gromacs mailing list that linear systems with same charges make the
system unstable? But is there
On 1/1/13 10:33 PM, Xu Dong Huang wrote:
Dear advanced gromac users,
I am trying to simulate a long linear chain of polymer using CG beads. (about
200 beads), all with same type charge interactions. (examples shown:) I read on
previous gromacs mailing list that linear systems with same
Dear Justin,
My .itp does not contain angles or dihedrals because we are simply interested
in the very simple generic case of a linear (what we assume by defining a
coordinate file of linear beads) polymer model. I will go through the tutorial
and try to see if it resolves my issue.
Xu Dong
First of all Happy New Year to everyone. Second, Justin I admire you. You keep
this forum alive and very well tended. Great job.Third, Parisa, try running
do_dssp with the flag -dt and pick an interval one or two orders of magnitude
smaller than the length of your simulation. That should do it.
On 1/1/13 10:46 PM, Xu Dong Huang wrote:
Dear Justin,
My .itp does not contain angles or dihedrals because we are simply interested
in the very simple generic case of a linear (what we assume by defining a
coordinate file of linear beads) polymer model. I will go through the tutorial
and
@Justin,
Does the philosophy described in your tutorial apply to CG martini bead models
where 1 bead describes the entire CO2 atom? (If I were to do that, assuming)
Xu Dong Huang
Chemical Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu
On Jan 1, 2013, at
On 1/1/13 10:51 PM, Xu Dong Huang wrote:
@Justin,
Does the philosophy described in your tutorial apply to CG martini bead models
where 1 bead describes the entire CO2 atom? (If I were to do that, assuming)
Presumably. As long as you satisfy the criteria mentioned in the tutorial
(moment
Dear GROMACS users,
A couple of days back I posted an issue which I have been facing, I
request you all to kindly help me..
I posted the following issue:
I ran a simulation using E_x as 1, 0.002, 0 i.e. i wanted a 0.002 V/nm
electric field strength. The simulation completed successfully. But
On 1/1/13 11:48 PM, ramesh cheerla wrote:
Dear Gromacs users,
I am performing umbrella sampling
simulations by selecting configurations with spacing window of 0.02nm from
pulling simulations with the following options in .mdp file to get PMF
along a
Dear Justin,
Thank you very much for your quick reply.
Regards,
Ramesh.
On Wed, Jan 2, 2013 at 10:24 AM, Justin Lemkul jalem...@vt.edu wrote:
On 1/1/13 11:48 PM, ramesh cheerla wrote:
Dear Gromacs users,
I am performing umbrella
27 matches
Mail list logo
