Re: [gmx-users] tutorial for liquid-solid simulation

On 9/20/12 7:55 AM, cuong nguyen wrote: Dear Gromacs Users, Could you please show me the tutorial for liquid-solid simulation? If it's not at http://www.gromacs.org/Documentation/Tutorials or found by Google, then it doesn't exist. -Justin -- Ju

Re: [gmx-users] Tutorial KALP-15 in DPPC

Thanks, got it.   Sincerely, Shima From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Friday, June 15, 2012 7:07 PM Subject: Re: [gmx-users] Tutorial KALP-15 in DPPC On 6/15/12 10:34 AM, Shima Arasteh wrote: > >  Thanks for your

Re: [gmx-users] Tutorial KALP-15 in DPPC

On 6/15/12 10:34 AM, Shima Arasteh wrote: Thanks for your reply. But one more question: what about when the applied lipid bilayer is POPC? Is this .top file (topol_dppc) useful yet? How come? You know, my main problem is that I don't know where this .top file come from? It was created wit

Re: [gmx-users] Tutorial KALP-15 in DPPC

From: Justin A. Lemkul To: Shima Arasteh ; Discussion list for GROMACS users Sent: Friday, June 15, 2012 6:57 PM Subject: Re: [gmx-users] Tutorial KALP-15 in DPPC On 6/15/12 10:25 AM, Shima Arasteh wrote: > >  Dear gmx users, > I am doing KALP15 in DPPC following the Justin t

Re: [gmx-users] Tutorial KALP-15 in DPPC

On 6/15/12 10:25 AM, Shima Arasteh wrote: Dear gmx users, I am doing KALP15 in DPPC following the Justin tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html . In the second step, the first command is grompp as follow: grompp -f mi

[gmx-users] Tutorial KALP-15 in DPPC

 Dear gmx users, I am doing KALP15 in DPPC following the Justin tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html . In the second step, the first command is grompp as follow:grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o e

Re: [gmx-users] Tutorial

Sara baretller wrote: Hi justin in the tutorail you have It is not necessary to run a complete energy minimization procedure on the bilayer, although you can if you want. The .tpr file contains information about bonding and periodicity, so it can, in a sense, be used to reconstruct "brok

Re: [gmx-users] Tutorial

Hi justin in the tutorail you have It is not necessary to run a complete energy minimization procedure on the bilayer, although you can if you want. The .tpr file contains information about bonding and periodicity, so it can, in a sense, be used to reconstruct "broken" molecules. when i tried

Re: [gmx-users] Tutorial

never mind , added both names and worked. did not work first time but then it did thank you On Thu, Aug 18, 2011 at 12:00 PM, Sara baretller < sarabiocomputat...@gmail.com> wrote: > > > what do i write on the top of the system.gro file before the number of the > molecules. do i add the name of p

Re: [gmx-users] Tutorial

what do i write on the top of the system.gro file before the number of the molecules. do i add the name of protein and the name of bilayer or somthing else to represent both systems in one system Thank you -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinf

Re: [gmx-users] Tutorial

Sara baretller wrote: Hi so i did Remove unnecessary lines (the box vectors from the KALP structure, the header information from the DPPC structure) and update the second line of the coordinate file (total number of atoms) accordingly. After i use the cat KALP_newbox.gro dppc128_whole.g

Re: [gmx-users] Tutorial

Sara baretller wrote: HI in the tutorial , it says that the script has the instructions to follow but when i opened the script i didn't find any instructions please what does 14 stands for and 5 perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat

Re: [gmx-users] Tutorial

Hi so i did Remove unnecessary lines (the box vectors from the KALP structure, the header information from the DPPC structure) and update the second line of the coordinate file (total number of atoms) accordingly. After i use the cat KALP_newbox.gro dppc128_whole.gro > system.gro when i check

Re: [gmx-users] Tutorial

HI in the tutorial , it says that the script has the instructions to follow but when i opened the script i didn't find any instructions please what does 14 stands for and 5 perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat thank you On Wed, Aug 17, 2011 at 4:19 PM, S

Re: [gmx-users] Tutorial

The author of InflateGRO, Christian Kandt, is now at Univ. of Bonn. All his work is here: http://www.csb.bit.uni-bonn.de/inflategro.html On 2011-08-17 03:03:50PM -0500, Sara baretller wrote: > Thank you > > yes i removed the Remove unnecessary lines ... i found the inflategro.pl >

Re: [gmx-users] Tutorial

ok i did find the script thank you On Wed, Aug 17, 2011 at 4:03 PM, Sara baretller < sarabiocomputat...@gmail.com> wrote: > Thank you > > yes i removed the Remove unnecessary lines ... i found the inflategro.pl > when i click on the rl inflategro.pl it gives me Firefox can't find the > server

Re: [gmx-users] Tutorial

Thank you yes i removed the Remove unnecessary lines ... i found the inflategro.pl when i click on the rl inflategro.pl it gives me Firefox can't find the server at inflategro.pl. On Wed, Aug 17, 2011 at 3:17 PM, Justin A. Lemkul wrote: > > > Sara baretller wrote:

Re: [gmx-users] Tutorial

Sara baretller wrote: I am doing the protein in lipid tutorial . http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html Pack the lipids around the protein, i dont see where is the script perl inflategro.pl I googled I

[gmx-users] Tutorial

I am doing the protein in lipid tutorial . http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html Pack the lipids around the protein, i dont see where is the script perl inflategro.pl I googled It and did not find it. Can you please send me the sc

[gmx-users] tutorial on channel simulations

Hi I want to perform water channel simulations, where channel is connected to bath of bulk water at standard thermodynamic conditions. The objective is to get the density distribution of water inside the channel , which is in equilibrium with the bath. Is there any tutorial specific to gromacs wh

Re: [gmx-users] tutorial of free energy calculations

HI Its not working for me either. But for free energy tutorials using GROMACS, I think the one written by Prof Mobley is like Bible. The link is as follows: http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial But the one written by Prof Alan Mark (who is now in Queensland Univ

[gmx-users] tutorial of free energy calculations

Dear GMX users, I don't know why I can't open the tutorial of free energy calculations on this website http://www.gromacs.org/Documentation/Tutorials. Can you open it? Thanks very much! All the best, fancy-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinf

Re: [gmx-users] tutorial for ionic liquid

Catarina Nunes wrote: Dear all, Do you have any tutorial for ? Best regards Catarina Gromacs tutorials can be found at: http://www.gromacs.org/Documentation/Tutorials If you don't find it there, try Google. If you don't find it there, it probably doesn't exist :) -Justin -- ===

[gmx-users] tutorial for ionic liquid

Dear all, Do you have any tutorial for ? Best regards Catarina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use

Re: [gmx-users] tutorial for membrane-bound systems

To: Discussion list for GROMACS users Sent: Thursday, March 20, 2008 2:00:49 AM Subject: [gmx-users] tutorial for membrane-bound systems Dear all, I would like to make MD simulations of a drug at the binding site of the receptor sorrounded by DPPC. pdb coordinate file

Re: [gmx-users] tutorial for membrane-bound systems

serdar durdagi <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Thursday, March 20, 2008 2:00:49 AM Subject: [gmx-users] tutorial for membrane-bound systems Dear all, I would like to make MD simulations of a drug at the binding site of the receptor sorrounded by DPPC. pdb

Re: [gmx-users] tutorial for membrane-bound systems

agi <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Thursday, March 20, 2008 2:00:49 AM Subject: [gmx-users] tutorial for membrane-bound systems Dear all, I would like to make MD simulations of a drug at the binding site of the receptor sorrounded by DPPC. pdb coordi

Re: [gmx-users] tutorial for membrane-bound systems

no official membrane tutorial, however. There is a ligand/receptor one out there somewhere I think? - Original Message From: serdar durdagi <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Thursday, March 20, 2008 2:00:49 AM Subject: [gmx-users] tutorial for membran

[gmx-users] tutorial for membrane-bound systems

Dear all, I would like to make MD simulations of a drug at the binding site of the receptor sorrounded by DPPC. pdb coordinate file of all DPPC units (189 units, 1 unit has 130 atoms) are described seperately. I was using Dundee PRODRG server for generating .itp and drgpoh2.pdb files for