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lower SOL ; Couple lipid
leaflets and SOL separately
tau-t= 0.1 0.1 0.1 ; Time constant for
temperature coupling
ref-t= 310 310 310 ; Desired temperature (K)
On Wed, Nov 13, 2013 at 4:07 PM, rajat desikan wrote:
>
solve
> this issue by regenerating velocities, or by running short cycles with the
> time step increasing from very small to normal.
>
> Hope it helps,
>
> Tsjerk
>
>
> On Wed, Nov 13, 2013 at 8:06 AM, rajat desikan >wrote:
>
> > Hi All,
> > Any suggestions?
&
Hi All,
Any suggestions?
Thanks,
On Mon, Nov 11, 2013 at 12:38 AM, rajat desikan wrote:
> Hi All,
> I am experiencing a few problems in membrane simulations wrt COM removal.
> I downloaded a 400 ns pre-equilibrated Slipid-DMPC membrane with all the
> accompanying files. I then car
iate any suggestions. Thank you.
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com> wrote:
>
>
> On 11/7/13 11:32 PM, Rajat Desikan wrote:
>
> > Dear All,
> > The setting that I mentioned above are from Klauda et al., for a POPE
> > membrane system. They can be found in charmm_npt.mdp in lipidbook (link
> > below)
> > http://lipidbook.b
Hi Justin,
Thanks for your time. I think I will use g_traj to spit out the P8
coordinates from upperP8_center_pbcnojump.xtc and write my own little MSD
routine :)
On Sat, Nov 9, 2013 at 11:36 PM, Justin Lemkul wrote:
>
>
> On 11/9/13 11:37 AM, rajat desikan wrote:
>
>> Hi
you do? Do you see any error in my workflow?
Thanks. Appreciate any suggestions...
On Sat, Nov 9, 2013 at 7:16 PM, Justin Lemkul wrote:
>
>
> On 11/9/13 5:24 AM, rajat desikan wrote:
>
>> Hi All,
>> I have a few older membrane simulations for which the COM for the upper
:
Group 0 (resname_DPPC_and_name_P8_and_res_com_z>4.3_0.000) has 192
elements
There is one group in the index
Reading frame 60 time 20600.000 Segmentation fault (core dumped)
Any ideas? Is there anything wrong with my workflow?
Thanks.
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Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa
tch description a month or so back, but I don't have that link
> to
> > hand).
> >
> > Mark
> >
> >
> > On Thu, Nov 7, 2013 at 8:45 PM, rajat desikan <[hidden
> > email]<http://user/SendEmail.jtp?type=node&node=5012329&i=0&g
hope to fix
> that in 5.0, but code is not written yet. I would probably use vdwtype =
> cut-off, vdw-modifier = potential-shift-verlet and rcoulomb=rlist=rvdw=1.2,
> but I don't run CHARMM simulations for a living ;-)
>
> Mark
>
>
> On Thu, Nov 7, 2013
Dear All,
Any suggestions?
Thank you.
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Thank you.
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Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
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Thank you, Justin!
I did intend to use h-bonds for the CHARMM36 simulations and all-bonds
elsewhere (depending on the FF). I just wanted some clarity before I
proceeded.
On Fri, Nov 1, 2013 at 1:49 AM, Justin Lemkul wrote:
>
>
> On 10/31/13 2:21 PM, rajat desikan wrote:
>
>
o simulate a POPC bilayer. Can someone with
experience please shed some light on this?
P.S.: Klauda et al., has posted their .mdp for POPE in gromacs on
lipidbook. Their .mdp constrains h-bonds
http://lipidbook.bioch.ox.ac.uk/uploads/package/CHARMM36/48-POPE-wurl/v1/charmm_npt.mdp
Thank you.
Thank you so much, Djurre.
I will do some tests with protein-membrane systems in mind and share it
with the community. I will see if I can reproduce the results in the 54A8
paper.
On Fri, Oct 25, 2013 at 1:01 PM, Djurre de Jong-Bruinink <
djurredej...@yahoo.com> wrote:
> Dear Raja
Thanks Justin!
If I manage to port it, I will share in the user contributions.
Regards,
On Thu, Oct 24, 2013 at 6:37 PM, Justin Lemkul wrote:
>
>
> On 10/24/13 9:00 AM, rajat desikan wrote:
>
>> Hi Justin,
>> Thanks for the comments.
>>
>> Since the script
24, 2013 at 6:01 PM, Justin Lemkul wrote:
>
>
> On 10/24/13 6:43 AM, rajat desikan wrote:
>
>> Dear all,
>> I want to use the Gromos54A8 FF in gromacs. They are available in gromos
>> format in http://www.gromos.net/main.pl ATB is yet to release it in
>> gromacs for
ort to gromacs...can you help me here?)
Thank you.
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Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
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Thank you, Mark!
On Wed, Oct 23, 2013 at 2:56 PM, Mark Abraham wrote:
> On Oct 23, 2013 7:24 AM, "rajat desikan" wrote:
> >
> > Hi,
> >
> > We recently had a software upgrade in our cluster from gromacs 4.5.4. to
> > gromacs 4.6.3.. I need to continu
later analysis?
I notice that I cannot use a 4.6.3 .cpt and .tpr in 4.5.4.
Any input will be appreciated. Thanks.
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Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
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wrote:
>
>
> On 10/9/13 7:03 AM, rajat desikan wrote:
>
>> Superb stuff, Justin. Thank you so much. Is it asking too much for a brief
>> list of the test systems that you used? Thanks again.
>>
>>
> We tested everything, at least in terms of representativ
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Prof. K.
rate
> > constant from the free energy. Hope that helps.
> >
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D
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Prof. K
Basic question: How do I verify that the right atoms were chosen in the
index file? There are a lot of atoms.
On Wed, Sep 25, 2013 at 9:52 PM, rajat desikan wrote:
> Thank you very much. My bilayers were initially built with packmol which
> is probably why z>6 worked. I will keep thi
Thank you very much. My bilayers were initially built with packmol which is
probably why z>6 worked. I will keep this in mind.
On Wed, Sep 25, 2013 at 9:46 PM, Teemu Murtola wrote:
> Hello,
>
> On Wed, Sep 25, 2013 at 5:48 PM, rajat desikan >wrote:
>
> > I have a dopc
Possible bug:
one of the values for comparison missing
g_select -s DOPC_0.5chl.gro -select 'resname DOPC and resname Cholesterol'
works perfectly fine. What is the problem?
Thank you.
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Dept. of Chemical Engi
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Hi Justin,
In a recent post
(http://gromacs.5086.x6.nabble.com/VDW-Cut-off-vs-Switch-with-CHARMM-force-field-td5010695.html;cid=1377399737789-944)
you commented that:
"Unless you can demonstrate that your changes in cutoffs do not produce
artifacts or lead to other inaccuracies using robust test s
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Thank you!
On Mon, Jul 15, 2013 at 6:29 PM, Justin Lemkul wrote:
>
>
> On 7/15/13 8:56 AM, rajat desikan wrote:
>
>> I guess, the more important question is whether the checkpoint file stores
>> the previous checkpoints as well. If it stores only the last checkpoint a
. otherwise, I would have used the snapshot from 18ns and
extended the simulation. Now, it looks like I will have to re-generate the
velocities and re-equilibrate the system.
On Mon, Jul 15, 2013 at 6:22 PM, rajat desikan wrote:
> Hi Justin,
> The checkpoint file has gone on to 20 ns. If
Hi Justin,
The checkpoint file has gone on to 20 ns. If I do a rerun, the simulation
will finish in one step.
On Mon, Jul 15, 2013 at 6:11 PM, Justin Lemkul wrote:
>
>
> On 7/15/13 8:38 AM, Rajat Desikan wrote:
>
>> Hi,
>> I have a 20 ns long trajectory which has beco
Hi,
I have a 20 ns long trajectory which has become corrupted beyond 18ns. I
have the full checkpoint file. Is there any way I can use mdrun and the .cpt
to rerun the simulation from 18ns and append it to the current .xtc (After I
have clipped the part beyond 18ns by trjconv)? I did not find the
a
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ontext that matters to you. You can probably get
> creative with editconf's translation options and come up with some fake
> trajectories via trjcat that test some edge cases relevant to what you want
> to do.
>
> Mark
>
>
> On Wed, May 22, 2013 at 7:40 PM, rajat desika
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Hi All,
I just read the paper pertaining to Gromos 54A8. I was wondering if the
force field files were available somewhere?
Thanks.
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Hi All
I have a membrane protein with a lot of alpha helices in it. I want to use
the 54a7 parameters for the protein and Kukol parameters (modified 53a6) for
the POPC membrane. Is this feasible? I know that there are issues with
combining widely different ffs, but these forcefields seem very simil
eply to this email, your message will be added to the discussion
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Hi All
I have a 100 ns lipid simulation for which I want the density profile. I
issued the following command
g_density -f martin_md_290K_100ns_tau1.xtc -n dppc.ndx -s
martin_md_290K_100ns_tau1.tpr -o water_density.xvg -b 5
The program fails with the following message
Selected 3: 'Water'
Last
Hi All,
Is there a convenient method to selectively make an index file containing
the upper leaflet and the lower leaflet of a DPPC bilayer?
Thanks.
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I got the answer to whether we can implement CHARMM36 into gromacs...:)
thanks
http://www.gromacs.org/Downloads/User_contributions/Force_fields
I still want your opinion on whether it is the best ff for simulating a
membrane-protein system, and if any modifications to the ff are necessary?
Thanks
So CHARMM36 would be the best ff for a long membrane protein simulation?
Is it possible to integrate CHARMM36 into Gromacs?
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Thanks for the quick and detailed replies Justin :) This helped clear some
doubts I had.
I thought all Charmm ff were compatible in Gromacs? Which Charmm ff were you
referring to?
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Se
"54A7 also introduced changes to the Gromos96 lipid parameters"
How will this change my inclusion of the berger lipid parameters? Any thing
that I should pay special attention to? Are there other lipid parameters
more compatible?
I heard from a faculty member at our Institute that the 53a6 is a bad
Hi all...
I heard that gromos 54a7 ff is much better for simulations than 53a6. i have
a membrane protein system. To simulate it, should I include the berger lipid
parameters manually as shown in justin Lemkul's membrane protein tutorial?
Thanks
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=1000)...does this have any bearing on my simulations?
On Mon, Nov 21, 2011 at 3:05 AM, Justin A. Lemkul wrote:
>
>
> rajat desikan wrote:
>
>> Justin,
>> Should i turn off charges on the methane molecules? I have left them on.
>>
>>
> What force field are yo
Justin,
Should i turn off charges on the methane molecules? I have left them on.
On Mon, Nov 21, 2011 at 12:32 AM, Justin A. Lemkul wrote:
>
>
> rajat desikan wrote:
>
>> My simulations are for 10 ns in each window. There is a lot of noise in
>> my wham too. I am enc
Oh lovely...thanks for the quick reply Justin :)...
On Sat, Nov 19, 2011 at 10:57 PM, Justin A. Lemkul wrote:
>
>
> rajat desikan wrote:
>
>> Hi
>> I am a new gromacs user. I just completed Justin's umbrella sampling
>> tutorial. I am doing a PMF calcula
apart)...can you
please tell me how to correct this?
Thanks
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Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
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