On Mon, May 30, 2011 at 10:10 PM, Justin A. Lemkul wrote:
>
>
> mohsen ramezanpour wrote:
>
>> Dear Dr.Justin
>>
>> There is not any answer?
>>
>>
> Please have a bit of patience. I'm not your personal answer service. You
> just happened to catch me at a good time this morning and I was able to
Justin A. Lemkul wrote:
Ryan S Davis (rsdavis1) wrote:
I wanted to copy a bilayer into a grid of 2x2x1 replicas. I used
genconf and everything seemed to work fine exept that annoying feature
that the command does not reorder the molecule types, so I end up with
a .top file looking like this
Ryan S Davis (rsdavis1) wrote:
I wanted to copy a bilayer into a grid of 2x2x1 replicas. I used genconf and
everything seemed to work fine exept that annoying feature
that the command does not reorder the molecule types, so I end up with a .top
file looking like this...
1 #include "martini
I wanted to copy a bilayer into a grid of 2x2x1 replicas. I used genconf and
everything seemed to work fine exept that annoying feature
that the command does not reorder the molecule types, so I end up with a .top
file looking like this...
1 #include "martini_v2.1.itp"
2 #include "martini_v2
Mr Bernard Ramos wrote:
Hi Justin,
Thanks for the immediate response. I apologize but I don't have with me
the mdp and the top files at the moment. But I will have it e-mailed
once I get back to my working gromacs computer.
Yes, as I remember, the [moleculetype] at the bottom of the topol
Hi Justin,
Thanks for the immediate response. I apologize but I don't have with me the mdp
and the top files at the moment. But I will have it e-mailed once I get back to
my working gromacs computer.
Yes, as I remember, the [moleculetype] at the bottom of the topol.top was able
to identify
Mr Bernard Ramos wrote:
Hi everyone!
I added a residue on the gromacs 4.5.3 I have. I followed the
instructions as indicated in the "Adding A Residue to a Force Field"
with this link
_http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field?highlight=adding+residue_.
Hi everyone!
I added a residue on the gromacs 4.5.3 I have. I followed the instructions as
indicated in the "Adding A Residue to a Force Field" with this link
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field?highlight=adding+residue.
I added the residue to residu
Thanks for the recommendations everyone. I tried all of the mdp changes
recommended by Justin (increase rlist, rvdw, etc to 2.0; change
T-coupling to v-scale, and eliminate P-coupling). When I increased the
distance cutoffs, it ran about 30 ps then crashed instead of crashing
immediately. On
On 31/05/2011 10:54 AM, Justin A. Lemkul wrote:
Joshua L. Phillips wrote:
I've found that I often get LINCS warnings like this when starting from
highly extended conformations when using implicit solvent. The GBSA
surface tension combined with the lack of viscosity (due to the absence
of expli
On 31/05/2011 8:50 AM, Justin A. Lemkul wrote:
One option that might be advantageous is to use the all-vs-all kernels
for a speed upgrade. You can accomplish this with:
rlist = 0
nstlist = 0
rvdw = 0
rcoulomb = 0
rgbradii = 0
pbc = no
comm-mode = angular
You'd have to run with mdrun -pd (part
Joshua L. Phillips wrote:
I've found that I often get LINCS warnings like this when starting from
highly extended conformations when using implicit solvent. The GBSA
surface tension combined with the lack of viscosity (due to the absence
of explicit water) allows the protein to change conformat
I've found that I often get LINCS warnings like this when starting from
highly extended conformations when using implicit solvent. The GBSA
surface tension combined with the lack of viscosity (due to the absence
of explicit water) allows the protein to change conformation much faster
than LINCS lik
thanks ...
On Mon, May 30, 2011 at 5:03 PM, Justin A. Lemkul wrote:
>
>
> bharat gupta wrote:
>
>> Well, mine is a beta-barrel protein called Green Fluorescent Protein. In
>> such a case the movement of ion is very important. As the ion in side the
>> barrel can quench the fluorescence. That's w
bharat gupta wrote:
Well, mine is a beta-barrel protein called Green Fluorescent Protein. In
such a case the movement of ion is very important. As the ion in side
the barrel can quench the fluorescence. That's what I want to track..
You can probably address this with the methods I've descr
Well, mine is a beta-barrel protein called Green Fluorescent Protein. In
such a case the movement of ion is very important. As the ion in side the
barrel can quench the fluorescence. That's what I want to track..
On Mon, May 30, 2011 at 4:57 PM, Justin A. Lemkul wrote:
>
>
> bharat gupta wrote:
bharat gupta wrote:
Thanks a lot.. If I am not wrong SMD and Umbrella sampling will help me
in determining the binding affinity. So, my first objective can be
achieved with it.
Then what about the movement of ions into the barrel. Will it be
possible to track it with MD coz the movement of
Thanks a lot.. If I am not wrong SMD and Umbrella sampling will help me in
determining the binding affinity. So, my first objective can be achieved
with it.
Then what about the movement of ions into the barrel. Will it be possible to
track it with MD coz the movement of ion is very important in my
bharat gupta wrote:
Thanks for your reply..
Actually I came across a paper "Molecular Modeling of the RNA binding
N-terminal Part of Cowpea Chlorotic Mottle Virus coat Protein in
Solution with Phosphate ion"... This paper was published in 1996, by Dr.
David van der Spoel.. In this paper , t
Thanks for your reply..
Actually I came across a paper "Molecular Modeling of the RNA binding
N-terminal Part of Cowpea Chlorotic Mottle Virus coat Protein in Solution
with Phosphate ion"... This paper was published in 1996, by Dr. David van
der Spoel.. In this paper , they were trying to find out
bharat gupta wrote:
Hi,
I want to dock a barrel protein with phosphate ion , to look for the
sites where Phosphate ion binds... I searched the gmx list but I didn't
find much related threads..
You usually won't find instructions specifically tailored for your specialty
application. This
Hi,
I want to dock a barrel protein with phosphate ion , to look for the sites
where Phosphate ion binds... I searched the gmx list but I didn't find much
related threads..
I want to do the following things...
1) Simulate the binding of phosphate ion with a barrel protein. Here I do
not know where
Thanks Justin, this is very helpful. I'll attempt these fixes tomorrow.
Mike
On 5/30/2011 5:50 PM, Justin A. Lemkul wrote:
Michael D. Daily wrote:
Hi all,
I'm trying to run implicit solvent calculations in gromacs 4.5 with
the charmm forcefield. I am able to minimize successfully and
c
Michael D. Daily wrote:
Hi all,
I'm trying to run implicit solvent calculations in gromacs 4.5 with the
charmm forcefield. I am able to minimize successfully and compile for
When troubleshooting, it is always advisable to try the latest version (4.5.4)
to see if the problem is reproduci
Hi all,
I'm trying to run implicit solvent calculations in gromacs 4.5 with the
charmm forcefield. I am able to minimize successfully and compile for
mdrun, but soon after starting, mdrun complains about excessive rotation
in LINCS (see the error printed below that). I also include my mdp fi
Hi all,
I'm trying to run implicit solvent calculations in gromacs 4.5 with the
charmm forcefield. I am able to minimize successfully and compile for
mdrun, but soon after starting, mdrun complains about excessive rotation
in LINCS (see the error printed below that). I also include my mdp fi
IEEE e-Science 2011 Workshop on Interoperability in Scientific Computing
5th December 2011, Stockholm, Sweden.
http://www.comlab.ox.ac.uk/david.johnson/wisc11/
The seventh IEEE e-Science conference, sponsored by the IEEE Com
Andrew DeYoung wrote:
Hi,
I have tried to run a simulation of 1000 SPC/E water molecules. I have a
PDB file containing a 10 by 10 by 10 regular array (cube) of water
molecules, each separated by approximately 6 Angstroms. I used pdb2gmx to
convert the PDB file to GRO and topology, selecting
mohsen ramezanpour wrote:
Dear Dr.Justin
There is not any answer?
Please have a bit of patience. I'm not your personal answer service. You just
happened to catch me at a good time this morning and I was able to respond
quickly. I have my own work to do, you know.
On Mon, May 30, 20
Hi,
I am trying to implement parameters for boron because I am simulating a
carborane (cluster molecules of CH and BH units). This corresponds to a plastic
crystal phase and the shape is a icosahedra cage. In this kind of phase, the
molecules are arranged within a lattice, but they do not have rest
Hi,
I have tried to run a simulation of 1000 SPC/E water molecules. I have a
PDB file containing a 10 by 10 by 10 regular array (cube) of water
molecules, each separated by approximately 6 Angstroms. I used pdb2gmx to
convert the PDB file to GRO and topology, selecting the OPLS-AA force field
an
Dear Dr.Justin
There is not any answer?
On Mon, May 30, 2011 at 7:58 PM, mohsen ramezanpour <
ramezanpour.moh...@gmail.com> wrote:
> Yes,you are right
> I need to do more sampling.But the second attached file was just to
> transfer my mean :)
> My final PMF curve is the first attached file.
>
Yes,you are right
I need to do more sampling.But the second attached file was just to
transfer my mean :)
My final PMF curve is the first attached file.
Sorry for asking more questions..
Regarding my notes about windowses in last email and looking at FIRST
attached file:
Which one is my starting
Hi,
I want to dock a barrel protein with phosphate ion , to look for the sites
where Phosphate ion binds... I searched the gmx list but I didn't find much
related threads..
I want to do the following things...
1) Simulate the binding of phosphate ion with a barrel protein. Here I do
not know where
mohsen ramezanpour wrote:
Thank you.
no,I think the problem is not zero point.
Actually I maean some thing like this one.please have a look at new
attached file.
I just added 3 new windows in 0.3 - 0.8
But the whoe of my curve shifted upward.
There is another question:
Actually I pulled my
Thank you.
no,I think the problem is not zero point.
Actually I maean some thing like this one.please have a look at new attached
file.
I just added 3 new windows in 0.3 - 0.8
But the whoe of my curve shifted upward.
There is another question:
Actually I pulled my drug from 0.18 - 3.18
then,extra
mohsen ramezanpour wrote:
Thank you for your reply
Actually my system is not the same as tutorial.
Then you should not equate the results, or be concerned when things look
different. Every system is different.
I tried to obtain protein-drug delta G.
I obtained that.
Yes,you are right,si
Thank you for your reply
Actually my system is not the same as tutorial.
I tried to obtain protein-drug delta G.
I obtained that.
Yes,you are right,since I don't have good computaional systems I couldn't
run more than 1 ns for each windows.
when there are some minimum and maximum in our curve ,Ho
mohsen ramezanpour wrote:
Dear Dr.Justin
Regarding to PMF curve which resulted from Umbrella sampling:
I obtained the following curve.
Dose it mean?Because it is not similar to yours in tutorial :(
if yes,please let me know what is the Delta G value approximately?
Because I don't know differen
Dear Dr.Justin
Regarding to PMF curve which resulted from Umbrella sampling:
I obtained the following curve.
Dose it mean?Because it is not similar to yours in tutorial :(
if yes,please let me know what is the Delta G value approximately?
Because I don't know difference between which points is my
Tomy van Batis wrote:
Dear Gromacs users
I have a very strange problem when using pdb2gmx in the gromacs 4.5.3. I
looked up the mailing list but I can't find something similar.
I have in a .pdb file a crystalline substrate consisting of Si particles.
By running in previous gromacs version
Dear Gromacs users
I have a very strange problem when using pdb2gmx in the gromacs 4.5.3. I
looked up the mailing list but I can't find something similar.
I have in a .pdb file a crystalline substrate consisting of Si particles.
By running in previous gromacs version (i.e. gromacs 3.3) :
*pdb2g
On 2011-05-30 12.58, sulatha M. S wrote:
Hi,
I plan to simulate a aqueous surfactant system with Bromide ions using
the GROMOS 45a3 force field. As I understand Bromide ion has not been
parametrized in GROMOS. I came across a paper by David van der Spoel, on
"Encapsulation of Myoglobin in a Cety
Hi,
Here is a paper that may be useful:
http://jcp.aip.org/resource/1/jcpsa6/v134/i14/p144103_s1
Computation of methodology-independent single-ion solvation properties from
molecular simulations. III. Correction terms for the solvation free
energies, enthalpies, entropies, heat capacities, volum
Hello Sir,
Thanks for your reply sir. I will check to it.
With regards
M. Kavyashree
On Mon, May 30, 2011 at 4:59 PM, Tsjerk Wassenaar wrote:
> Hi Kavya,
>
> There is no way to correct for such things afterwards. But I would
> guess it's not much of a problem in your case. If a situation wit
Anirban Ghosh wrote:
Hello Justin,
Thanks for the reply.
Actually I am using the last frame .gro of a 3 micro-second run CGMD
simulation as the input for GridMatMD. But in the thickness plot the
positions of the protein depicted are not matching with what I am
visualizing through VMD. I sup
Thanks Justin for your advice, it was one of the mpi flags only which caused
the error.
regards,
Vivek
On 27 May 2011 17:39, Justin A. Lemkul wrote:
>
>
> vivek sharma wrote:
>
>> HI GMX-users,
>> I am trying to run a REMD simulation on my system. I have created 10 .tpr
>> files and fired the
Hi Kavya,
There is no way to correct for such things afterwards. But I would
guess it's not much of a problem in your case. If a situation with a
short distance is only transient, it is unlikely to affect the
simulation. On the other hand, you may have secondary, indirect
effects due to water orde
Hello Justin,
Thanks for the reply.
Actually I am using the last frame .gro of a 3 micro-second run CGMD
simulation as the input for GridMatMD. But in the thickness plot the
positions of the protein depicted are not matching with what I am
visualizing through VMD. I suppose this is because of some
Anirban Ghosh wrote:
Hi ALL,
I have simulated a CGMD system consisting of multiple copies of a CG
protein in a CG lipid bilayer using the MARTINI FF for the CG
definitions. Can I use GridMatMD program to calculate the area per lipid
and other properties in this CG system? Which parameters do
Sweta Iyer wrote:
Hi,
I am trying to insert my protein dimer complex in a membrane using the
g_membed tool.
I made an index group where I saved the monomers as separate groups and
mentioned the same groups in the .mdp file.
This should not be necessary. If both are protein, then they belong
Hi,
I plan to simulate a aqueous surfactant system with Bromide ions using the
GROMOS 45a3 force field. As I understand Bromide ion has not been
parametrized in GROMOS. I came across a paper by David van der Spoel, on
"Encapsulation of Myoglobin in a Cetyl Trimethylammonium Bromide Micelle
..." u
Hello Sir,
The difference between the rcolumb (1.4nm) and minimum image distance
that was obtained between two hydrogen HZ2 and HZ3 atoms of 2 lysine
residues (1.39714nm) is 0.00286nm = 0.0286Ang,
Since this distance is smaller than bond distance between hydrogen and
nitrogen which is ~1.0Ang, So
Hi ALL,
I have simulated a CGMD system consisting of multiple copies of a CG protein
in a CG lipid bilayer using the MARTINI FF for the CG definitions. Can I use
GridMatMD program to calculate the area per lipid and other properties in
this CG system? Which parameters do I need to alter in the inp
Dear Gromacs users,
I am perturbing a PDB structure in a certain way, and then wish to
obtain a topology for Gromacs minimization, simulation and analysis.
The structure contains some disulfide bonds; however, pdb2gmx guesses
them incorrectly as the distances between the Sulfur atoms change.
E
Ah okay. Sorry then.
But if its only the atom names that dont match, isn't it worth a try to either
name them correctly in the pdb file(maybe via a little script) or to adjust the
names in the topology file so they match the pdb? (I know, very simple-hearted
question.)
_
Hi,
I am trying to insert my protein dimer complex in a membrane using the
g_membed tool.
I made an index group where I saved the monomers as separate groups and
mentioned the same groups in the .mdp file.
However, it gives me an error saying "Freeze value does not match :There
are 2 freeze groups
I know this, but this file cannot be used because the atom name is quite
different from gromacs CHARMM36 topol library.
At 2011-05-30，"Rausch, Felix" wrote:
Check this link given by another (unknown) mailing list user yesterday (Topic
name:about POPC in Gromacs )!
http://terpconnect.umd.ed
Check this link given by another (unknown) mailing list user yesterday (Topic
name: about POPC in Gromacs )!
http://terpconnect.umd.edu/~jbklauda/research/download.html
Von: gmx-users-boun...@gromacs.org im Auftrag von albert
Gesendet: So 29.05.2011 21:23
An: D
Thank you so much for kind helps. I will try it
At 2011-05-30，"Jianguo Li" wrote:
I equilibrated the system for about 20ns at 300K.
Jianguo
From: albert
To: Jianguo Li
Cc: Discussion list for GROMACS users
Sent: Monday, 30 May 2011 14:52:23
Subject: Re:Re: Re: [gmx-users] is it possible to
Hi Lishan,
Your mail would be a bit more readable with more structure...
Anyway, it says in the manual you can't do perturbation on the
multiplicity. That makes sense, because interpolation from 1 to 3 goes
through a whole series of rational numbers, but you can't have
non-integer periods... If y
Hey,
>> If a rename atom A into B, it will mix the old atom B which already there
>> before A renamed into B. However, if the old atom B also need to be renamed
>> into C. Here is the problem , command cannot recognize this atom B is the
>> new generated or the old atom B. Of course, those atom B
Thank you so much for your such kind helps. I will try it.
At 2011-05-30，"Jianguo Li" wrote:
I equilibrated the system for about 20ns at 300K.
Jianguo
From: albert
To: Jianguo Li
Cc: Discussion list for GROMACS users
Sent: Monday, 30 May 2011 14:52:23
Subject: Re:Re: Re: [gmx-users] is it
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