Dear jkrieger
I used 2 times trjconv tool:
1) trjconv -f npt.xtc -s npt.tpr -n index.ndx -o 2npt.xtc -pbc nojump
2) trjconv -f 2npt.xtc -s npt.tpr -n index.ndx -o 3npt.xtc -pbc mol -center
Dear Mark
I selected all lipid atoms for centering.
With my manner, pbc problem was solved just for lip
dear gromacs users
im using gromacs to make CS2 MD programs i made pdb file (by converting mol
file to pdb file) and rtp file for CS2this is what i made
COMPNDUNNAMEDAUTHORGENERATED BY OPEN BABEL 2.3.2HETATM1 C LIG
1 19.882 -4.263 -0.027 1.00 0.00 C HETATM
Hi,
I also want to try :)
Best regards,
~Thu
On Wed, Oct 23, 2013 at 11:39 PM, houyang chen wrote:
> Hi Kevin
> Can I have a try?
> Best
> Houyang
>
>
> On Wed, Oct 23, 2013 at 12:30 PM, Villarealed wrote:
>
> > Sound nice. I would like to try out.
> > Could You please set up an account for me
got it. Thanks Justin.
On Wed, Oct 23, 2013 at 4:37 PM, Justin Lemkul wrote:
>
>
> On 10/23/13 4:28 PM, Dina Mirijanian wrote:
>
>> Hello,
>> I am trying to convert a protein+ATP+water+ion system pdb into gromacs
>> files. I need to use the existing water and ion coordinates. I can
>> conver
On 10/23/13 4:28 PM, Dina Mirijanian wrote:
Hello,
I am trying to convert a protein+ATP+water+ion system pdb into gromacs
files. I need to use the existing water and ion coordinates. I can
convert the protein part using pdb2gmx and grompp fine. But, I do not know
how to process the solvent a
Hello,
I am trying to convert a protein+ATP+water+ion system pdb into gromacs
files. I need to use the existing water and ion coordinates. I can
convert the protein part using pdb2gmx and grompp fine. But, I do not know
how to process the solvent and ion coordinates separately and combine them
t
Center on a particular lipid? Or head group?
Mark
On Oct 23, 2013 6:13 PM, "shahab shariati"
wrote:
> Dear gromacs users
>
> My system contains DOPC + CHOLESTEROLO + WATER + drug molecules in a
> rectangular box.
>
> I put drug molecule in 2 position: a) drug in the center of bilayer
> membrane,
I usually use -pbc nojump for my protein simulations and this works every
time.
> Dear gromacs users
>
> My system contains DOPC + CHOLESTEROLO + WATER + drug molecules in a
> rectangular box.
>
> I put drug molecule in 2 position: a) drug in the center of bilayer
> membrane, b) drug inside water
I ran into this, you basically should determine your time frame, and install 4.5.4 if its a problem local (only 1-2 hours), to finish the work, otherwise you need to start from scratch. But I did this with older versions, so do not know about higher versions (such as if the programmers eliminated
On 10/23/13 12:44 PM, Michelangelo Scordino wrote:
Sorry, i should want to be delete my contact from mailing list.
thanks
Unsubscribing is explained in the footer of every email that hits the list:
"* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to
Sorry, i should want to be delete my contact from mailing list.
thanks
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Hi Kevin
Can I have a try?
Best
Houyang
On Wed, Oct 23, 2013 at 12:30 PM, Villarealed wrote:
> Sound nice. I would like to try out.
> Could You please set up an account for me?
> Regards,
> Eduardo Villarreal
> villarea...@hss.edu
>
> -
> Eduardo Villarreal Ramírez
> Postdoctoral Research F
Sound nice. I would like to try out.
Could You please set up an account for me?
Regards,
Eduardo Villarreal
villarea...@hss.edu
-
Eduardo Villarreal Ramírez
Postdoctoral Research Fellow
Mineralized Tissue Laboratory,
Hospital for Special Surgery.
--
View this
Hi Kevin
I would like to try it out.. Let me know the procedure to create an
account..
Regards
Ash
On Tuesday, October 22, 2013, Kevin Chen wrote:
> Hi Everyone,
>
> I'm writing to let you guys know that we have developed a web-based tool MD
> simulation tool for GROMACS. It is a software pack
Dear gromacs users
My system contains DOPC + CHOLESTEROLO + WATER + drug molecules in a
rectangular box.
I put drug molecule in 2 position: a) drug in the center of bilayer
membrane, b) drug inside water molecules in top leaflet.
For both positions, I did energy minimization successfully with fo
I'd like to check it out too
On Wed, Oct 23, 2013 at 8:45 AM, Ehsan Sadeghi wrote:
> Hi Kevin,
>
> It seems interesting. I would like to try it out. May I have an account?
>
> Best regards,
> Ehsan
>
>
>
> - Original Message -
> From: "Kevin Chen"
> To: "Discussion list for GROMACS use
Please could I have an account too.
> Hi Everyone,
>
> I'm writing to let you guys know that we have developed a web-based tool
> MD
> simulation tool for GROMACS. It is a software package primarily developed
> for biological MD and offers a huge amount of possible options and
> settings
> for ta
Hi Kevin,
It seems interesting. I would like to try it out. May I have an account?
Best regards,
Ehsan
- Original Message -
From: "Kevin Chen"
To: "Discussion list for GROMACS users"
Sent: Tuesday, October 22, 2013 7:34:10 AM
Subject: [gmx-users] a new GROMACS simulation tool
Hi Eve
Hi,
Sounds very interesting. Can I have a test account, please?
The Lindahl group has some related work going on at
http://copernicus-computing.org/, automating large-scale simulation
workflows. I'm not sure yet whether we have any synergies! :-)
Cheers,
Mark
On Tue, Oct 22, 2013 at 4:34 PM,
There shouldn't be a problem for that. BTW, can you also enter a ticket at
Daigrid.org for this matter?
Thanks
-Kevin
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of rajat desikan
Sent: Wednesday, October 23, 2013 1:24 AM
To: Di
me to
On Wed, Oct 23, 2013 at 12:27 PM, Thales Kronenberger <
kronenberg...@gmail.com> wrote:
> I also would like to try
>
>
>
>
> 2013/10/23 Gloria Saracino
>
> > Dear Kevin,
> > I'm Gloria Saracino from the Center of Nanomedicine and Tissue
> Engineering
> > of the Hospital of Niguard
On 10/23/13 7:20 AM, Archana Sonawani-Jagtap wrote:
Hi all,
I have never performed TFE-water simulation therfore I want to know after
inserting the peptide in the pre-equilibrated TFE-water mixture, do we need
to adjust the number of TFE or water molecules ?
That depends on how you construc
On 10/22/13 9:57 PM, Nimmy McNimmerson wrote:
I have some simulations of inserting a probe molecule into a bilayer. Some
molecules work fine. However, a certain class of molecules is taking an
absurdly long time to run the exact same simulation, even though I energy
minimized the molecules i
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 continue an earlier simulation that had been
> run
>
Hi all,
I have never performed TFE-water simulation therfore I want to know after
inserting the peptide in the pre-equilibrated TFE-water mixture, do we need
to adjust the number of TFE or water molecules ?
or should I directly add ions to this system and run the production run.
Any suggestion i
I also would like to try
2013/10/23 Gloria Saracino
> Dear Kevin,
> I'm Gloria Saracino from the Center of Nanomedicine and Tissue Engineering
> of the Hospital of Niguarda Ca' Granda in Milan, Italy.
>
> I'm interested into knowing more about this new web based toolas I use MD
> everyday.
>
By "crash" I meant "explode" not "DD is impossible." Explosions don't
happen because of parallelism, they happen because the steps are too large
for the size of the forces. The forces required to stably expand a box from
20A to 70A seem likely to be so large that I am very skeptical that you
could
If the job is not "very parallel", it will not crash.
It is better to preequilibrate in NVT beforehand. Cyclopropylchloride
is probably a liquid at 290K, if the model is parametrized reasonably.
So it should not phase-separate.
Vitaly
On Wed, Oct 23, 2013 at 11:29 AM, Mark Abraham wrote:
> On
On Oct 23, 2013 5:34 AM, "Nilesh Dhumal" wrote:
>
> Hello,
>
> I am running a NPT simulation for cyclopropylchloride(1) in
> 50%water(100)+50%ethanol(100) using opls force field parameter .
>
> After equilibration box size increases from 20 A to 70 A.
Really? Seems wildly unlikely to have occurre
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 continue an earlier simulation that had been run
> in 4.5.4. using the .cpt, .tpr and .mdp.
>
> Are there any issues with continuing thes
Dear Kevin,
I'm Gloria Saracino from the Center of Nanomedicine and Tissue Engineering of
the Hospital of Niguarda Ca' Granda in Milan, Italy.
I'm interested into knowing more about this new web based toolas I use MD
everyday.
Let me know what I have to do.
Regards,
Gloria Saracino
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