On 5/7/12 1:01 AM, Anirban Ghosh wrote:
On Mon, May 7, 2012 at 10:17 AM, Bala S mailto:think_bey...@aol.com>> wrote:
Justin and Anirban,
I have another query on membrane simulation following your tutorials.
How do I insert only a part of protein into the lipid bilayer and carry
On Mon, May 7, 2012 at 10:17 AM, Bala S wrote:
> Justin and Anirban,
>
> I have another query on membrane simulation following your tutorials.
>
> How do I insert only a part of protein into the lipid bilayer and carryout
> the simulation?
>
editconf with -box option helps you to orient your pro
Justin and Anirban,
I have another query on membrane simulation following your tutorials.
How do I insert only a part of protein into the lipid bilayer and carryout
the simulation?
Thanks
Bala S
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Justin and Anirban,
My phase-2 equibration run was completed and I could see SOL molecules moved
close to the head groups of lipids. Now, I'm confident that I can apply this
rocedure on other proteins as well.
Thank you so much both you for walking along through the session.
Bala S
--
View this
Hi Justin and Anirban,
I've seen that most of the SOL molecules movin towards the head groups after
NVT equilibrium run as mentioned in Justin's. I'm wiating for my NPT run to
complete. Hopefully I can see all of them aliging over the headgroups.
Thanks
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On Fri, Apr 27, 2012 at 7:37 PM, Justin A. Lemkul wrote:
>
>
> On 4/27/12 10:00 AM, Bala S wrote:
>
>> Anirban,
>>
>> Exactly.. That's the gap (either side of the leaflets) I was mentioning
>> about. I'll try EM and check itagain.
>>
>>
> EM won't fill in solvent gaps. If you're using my protoco
On 4/27/12 10:00 AM, Bala S wrote:
Anirban,
Exactly.. That's the gap (either side of the leaflets) I was mentioning
about. I'll try EM and check itagain.
EM won't fill in solvent gaps. If you're using my protocol for increasing the C
radius in vdwradii.dat, then a small gap is normal and
Anirban,
Exactly.. That's the gap (either side of the leaflets) I was mentioning
about. I'll try EM and check itagain.
Thanks.
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Sent from the GROMACS Users Forum mailing l
On Fri, Apr 27, 2012 at 7:00 PM, Bala S wrote:
> Anirban,
>
> Thank you. You guys are doing miracles with the biomolecules and solving
> almost all of my problems.
>
> I have followed your suggestion and could see now some more SOL molecules
> by
> increasing the z value.
>
> But I am seeing a su
Anirban,
Thank you. You guys are doing miracles with the biomolecules and solving
almost all of my problems.
I have followed your suggestion and could see now some more SOL molecules by
increasing the z value.
But I am seeing a substantial gap between the surface of the lipid bilayer
and added S
On Fri, Apr 27, 2012 at 6:31 PM, Bala S wrote:
> Justin,
>
> OOPS!!
> Sorry for that.. Now I could realize it.
> Following up.. I have done further iterations with inflategro and reached
> 0.62 nm^2 which similar to what you have explained in the tutorial.
>
> Now, I could see the lipid bilayer r
Justin,
OOPS!!
Sorry for that.. Now I could realize it.
Following up.. I have done further iterations with inflategro and reached
0.62 nm^2 which similar to what you have explained in the tutorial.
Now, I could see the lipid bilayer really shrinked and no SOL molecules are
seen in between. Now th
On 4/27/12 8:38 AM, Bala S wrote:
Thanks Justin and Anirban for taking this long in TM simulations.
I'm following Justin's tutorial majorly and taking some clues from Anirban's
too when I need further clarification.
From both of your guidelines I could understand wht I should be doing before
Thanks Justin and Anirban for taking this long in TM simulations.
I'm following Justin's tutorial majorly and taking some clues from Anirban's
too when I need further clarification.
>From both of your guidelines I could understand wht I should be doing before
solvating the system. Now, I have a q
On Fri, Apr 27, 2012 at 4:59 PM, Justin A. Lemkul wrote:
>
>
> On 4/27/12 6:40 AM, Bala S wrote:
>
>> Thanks for the reply.
>>
>> I'm following the tutorial.
>>
>>
> Please clarify whether you're using Anirban's or mine. Now that two
> exist, people will have to be a fair bit more specific :)
>
On 4/27/12 6:40 AM, Bala S wrote:
Thanks for the reply.
I'm following the tutorial.
Please clarify whether you're using Anirban's or mine. Now that two exist,
people will have to be a fair bit more specific :)
In your system, to solvate it you have the values that was used during the
p
Thanks for the reply.
I'm following the tutorial.
In your system, to solvate it you have the values that was used during the
protien insertion into the bilayer. Following it, I have used the following
commandfor my system where the protein is very much smaller than the length
of the bilayer.
$ e
On 4/27/12 6:04 AM, Anirban Ghosh wrote:
On Fri, Apr 27, 2012 at 3:27 PM, Bala S mailto:think_bey...@aol.com>> wrote:
Thank you for that clarification.
I found that there were SOL molecules in .top file. I could run the EM now.
Coming to the Solvation step, I'm facing a problem
On Fri, Apr 27, 2012 at 3:27 PM, Bala S wrote:
> Thank you for that clarification.
>
> I found that there were SOL molecules in .top file. I could run the EM now.
>
> Coming to the Solvation step, I'm facing a problem.
>
> I have made the mentioned change (0.15 to 0.375 for C) in the vdwradii.dat
Thank you for that clarification.
I found that there were SOL molecules in .top file. I could run the EM now.
Coming to the Solvation step, I'm facing a problem.
I have made the mentioned change (0.15 to 0.375 for C) in the vdwradii.dat
locally.
While adding the solvent molecules, what command
On Fri, Apr 27, 2012 at 1:01 PM, Bala S wrote:
> Dear Justin
>
> Thanks for the explanation.
>
> I am following your tutorial of KALP membrane simulation. I am stuck in
> between two steps of InflateGRO. After the first step, the tutorial
> requests
> to perform EM. Should I be running grompp wit
Dear Justin
Thanks for the explanation.
I am following your tutorial of KALP membrane simulation. I am stuck in
between two steps of InflateGRO. After the first step, the tutorial requests
to perform EM. Should I be running grompp with new system_inflated.gro file
to generate a new .tpr file for
Hello Bala,
Yes, exactly as Justin said it represents just a workflow where a GPCR
protein (here B2AR) has been taken as an example. I mentioned it as a GPCR
tutorial because many often inquire about GPCR MD simulations only in the
forum. But it can be adapted for other membrane proteins as well.
Looks I got to the party late (at a conference with limited time to do emails).
As a shameless self-plug, we recently published a soup-to-nuts protocol paper
for GPCR + POPC + ligand in Gromacs 4.5.x and CHARMM27/36/CGenFF.
Our timescales are on the order 100+ns.
20ns/day is possible on 100K ato
On 4/26/12 9:35 AM, Bala S wrote:
Dear Anirban,
Thanks for the tutorial you have created for the newbies like me to follow.
I wonder the tutorial is only for the GPCRs not applicable for other
membrane proteins?
Tutorials present possible workflows. Anirban's tutorial does not significant
Dear Anirban,
Thanks for the tutorial you have created for the newbies like me to follow.
I wonder the tutorial is only for the GPCRs not applicable for other
membrane proteins?
I also have another question about slecting a lipidbilayer, what is the
criteria is selecting it, for instance popc, d
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