Thanks for that comment.
I've another query during inflating step in Justin's tutorial.
In my case, during the inflation, 4 lipids from the upper and 2 lipids from
the lower leaflets were removed.
Would there be a problem in this sort non-uniform deletion (I mean like 4
from upper and 4 from lowe
Dear all user,
I'm a gromacs beginner and have a quick question.
I installed gromacs 4.5.5 online on ubuntu12.04.
How do I check that it is correctly installed?
and,
What is The gromacs tutorial output files?
I could not get them tpr file.
Please help me.
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Dear Gromacs Users,
I don't know what is the quantity of -cut in g_clustsize for different systems,
exactly!
May I ask you to help me, Please?
Best Regards
Sara
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Oh ! Thnaks
I saw that table, the angle_restrain option is there but not constraints .
Anyway if suppose, I fix the distance between the two terminal atoms
of the molecule, the angle will eventually be fixed at a particular
given value. Is that the logic ?
Actually I searched for this problem so ma
On 24/07/2012 3:21 PM, tarak karmakar wrote:
Dear All,
I am constraining one angle in my protein sample by incorporating " [
constraints ]" block in topology file as
[ constraints ]
; index1 index2 index3 funct angle
6064 6063 6065 1 180.0
while doing that its showing the fo
Dear All,
I am constraining one angle in my protein sample by incorporating " [
constraints ]" block in topology file as
[ constraints ]
; index1 index2 index3 funct angle
6064 6063 6065 1 180.0
while doing that its showing the following error
Program grompp, VERSION 4.5.5
Sou
On 24/07/2012 2:37 PM, tarak karmakar wrote:
Dear All,
In a protein simulation I imposed one bond constraint by
incorporating the "[constraints]" block in topology file. On the other
hand in .mdp file I have imposed constraints for the covalent hydrogen
bonds by implementing the LINCS algo
On 24/07/2012 2:57 PM, J Peterson wrote:
Hi Justin,
That works really fine and thanks.
Now, how can I add additional SOL molecules only one side of the bilayer
(either upper or lower)? Since my protein binds at the outer side
(extracellular region) of the membrane I can only fill the upper
(ext
Hi Justin,
That works really fine and thanks.
Now, how can I add additional SOL molecules only one side of the bilayer
(either upper or lower)? Since my protein binds at the outer side
(extracellular region) of the membrane I can only fill the upper
(extracellular) region with SOL molecules inste
Dear All,
In a protein simulation I imposed one bond constraint by
incorporating the "[constraints]" block in topology file. On the other
hand in .mdp file I have imposed constraints for the covalent hydrogen
bonds by implementing the LINCS algorithm. After a short equilibration
run I see the
On 2012-07-23 02:34:31PM -0300, Sebastien Cote wrote:
>
> There is not much difference when using DispCorr or not. At least on the same
> time scale as the simulation with switch cutoff from 0.8 to 1.2 nm and on the
> same time scale.
>
> Should DispCorr be used in all membrane simulations? I
Dear gmx-users
I am trying to calculate the optical rotation of a molecule in solution. There
are several examples of this in the literature where they take snapshots of
molecule at intervals throughout the trajectory, calculate optical rotation,
and average them to get a solvated optical rotat
On 7/23/12 2:47 PM, Debashis Sahu wrote:
Dear all user,
I'm a gromacs beginner and have a quick question.
Can anyone tell me about the .hdb file description, e.g. '8' indictes
no.of kind of hydrogen, ARG is residue name, after that 1st column
indicates the no. of hydrogens fo
Dear all user,
I'm a gromacs beginner and have a quick question.
Can anyone tell me about the .hdb file description, e.g. '8' indictes
no.of kind of hydrogen, ARG is residue name, after that 1st column
indicates the no. of hydrogens for each type but 2nd column's
indication is not
There is not much difference when using DispCorr or not. At least on the same
time scale as the simulation with switch cutoff from 0.8 to 1.2 nm and on the
same time scale.
Should DispCorr be used in all membrane simulations? I thought that we should
always use this correction.
Thanks,
Se
On 7/23/12 12:53 PM, SatyaK wrote:
Thanks for the reply. In fact, I had followed the fixed format of Gromacs
during the conversion. Below is the sample data, where I have just the
{X,Y,Z}:
2171OHX OW 5231 -0.543 -2.5801000.000
2171OHXHW1 5232 -0.510 -2.5471000.110
Z coordinate
Thanks for the reply. In fact, I had followed the fixed format of Gromacs
during the conversion. Below is the sample data, where I have just the
{X,Y,Z}:
2171OHX OW 5231 -0.543 -2.5801000.000
2171OHXHW1 5232 -0.510 -2.5471000.110
Z coordinate is 1000.000 and 1000.110 respectively in
On 7/23/12 12:32 PM, SatyaK wrote:
Hello All,
I have an issue with converting a .dat file into GRO format and viewing it
in VMD. Say, we have {x, y,z} ={0,0,1} in A.
> Converted GRO file (in nm): 171OHX OW 5000 0 01000.000
The Z coordinate has 8 places which is apt as per t
Hello All,
I have an issue with converting a .dat file into GRO format and viewing it
in VMD. Say, we have {x, y,z} ={0,0,1} in A.
> Converted GRO file (in nm): 171OHX OW 5000 0 01000.000
The Z coordinate has 8 places which is apt as per the Gro format.
However,when VMD reads th
On 7/23/12 9:54 AM, Christian Blouin wrote:
Hello,
I have been running a simple simulation where I replace 150
water molecules in a waterbox with a lipid called DPC to create
micelles. This simulation is working fine and I'm getting decent
micelles fairly quickly. I am now trying to do
Hello,
I have been running a simple simulation where I replace 150
water molecules in a waterbox with a lipid called DPC to create
micelles. This simulation is working fine and I'm getting decent
micelles fairly quickly. I am now trying to do the same, but with a
small peptide in the simula
Exactly so. But in the ffbonded.itp file there are two columns,
equilibrium bond length and Kb . So evenif I give zero then it won't
affect the bond .
Thanks a lot for the reply, it's working fine now .
On Mon, Jul 23, 2012 at 6:02 PM, Justin Lemkul wrote:
>
>
> On 7/23/12 8:31 AM, tarak karmakar
On 7/23/12 8:31 AM, tarak karmakar wrote:
Thanks for the reply.
But then what should I give as Kb [ bond stretching constant ] in the
ffbonded.itp file ? should I give 00.000 there or something else ???
Constraints make bonds rigid. The force constant is irrelevant.
-Justin
On Mon, Jul 2
Thanks for the reply.
But then what should I give as Kb [ bond stretching constant ] in the
ffbonded.itp file ? should I give 00.000 there or something else ???
On Mon, Jul 23, 2012 at 4:11 PM, Justin Lemkul wrote:
>
>
> On 7/23/12 2:39 AM, tarak karmakar wrote:
>>
>> Dear All,
>>
>>
>>In my
On 7/23/12 7:53 AM, J Peterson wrote:
Thank you so much for that, Justin.
Now I could expand the bilayer.
I've another query. My protein has a small N-terminal portion embedded in
the membrane, I would like to insert only this part into the membrane during
'packing the lipid around the protei
Thank you so much for that, Justin.
Now I could expand the bilayer.
I've another query. My protein has a small N-terminal portion embedded in
the membrane, I would like to insert only this part into the membrane during
'packing the lipid around the protein' step in your tutorial. Initially I
was
On 7/23/12 5:31 AM, J Peterson wrote:
Hi Justin,
Thanks for all your help to get me through membrane simulations.
I've a problem to be solved. I need a long and thick membrane to simulate a
big protein. The longest bilayer that I can download from Tieleman's website
is 64 molecules long.
How
On 7/23/12 2:39 AM, tarak karmakar wrote:
Dear All,
In my simulation I want to fix the S=O bond length of SO2, but the
angle has to be kept flexible. So I search for the distance restraints
in gromacs mailing list and
accordingly I have incorporated the distant_restraints block in the
topo
Hi Justin,
Thanks for all your help to get me through membrane simulations.
I've a problem to be solved. I need a long and thick membrane to simulate a
big protein. The longest bilayer that I can download from Tieleman's website
is 64 molecules long.
How can I make (double or triple the bilayer)
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