Dear Justin,
Thank you very much for your quick reply.
Regards,
Ramesh.
On Wed, Jan 2, 2013 at 10:24 AM, Justin Lemkul wrote:
>
>
> On 1/1/13 11:48 PM, ramesh cheerla wrote:
>
>> Dear Gromacs users,
>>
>> I am performing umbrella samplin
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 axis
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
now
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
@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 10:
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 tr
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.
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
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 charg
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 an
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.i
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 /home/parisa/parisa/share/gro
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 2:01 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,
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 "do
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 :
> Hi Leandro!
>
> Actually I need such
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 parameter(s
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 'N*
Thanks.
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
Cc:
Sent: Tuesday, January 1, 2013 7:27 PM
Subject: Re: [gmx-users] LINCS WARNING - Protein-Membrane-system
On 1/1/13 10:53 AM, Shima Arasteh wrote:
>
>
>
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
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 mini
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
- Orig
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 "
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/WA
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) LINC
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 af
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
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