[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

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 -- View this message in context: http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS

[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

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 --

[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

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 -- View this message in context: http://

[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

Anirban, Exactly.. That's the gap (either side of the leaflets) I was mentioning about. I'll try EM and check itagain. Thanks. -- View this message in context: http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4933996.html Sent from the GROMACS Users Forum mailing l

[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

SOL molecules in the visualizer. Is it normal or I have to do something about it? Thanks Bala S -- View this message in context: http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4933923.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com

[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

the issue I would like to have clarification on is that only 163 SOL molecules were added up and down which looks very scarce for the simulation. What is the solution? Bala S -- View this message in context: http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4933854

[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

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

[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

es to whole length or how to remove not-solvated part of lipids? Thanks Bala S -- View this message in context: http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4933536.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing

[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

f SOL molecules. I guess I'm worng somehere. Thanks. Bala S -- View this message in context: http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4933479.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list

[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

EM or should I perform EM with em.tpr which was generated some time back in the tutorial? The latter ran EM but the former shows error 'number of coordinates in coordinate file (system_inflated.gro, 6438) does not match topology (topol.top, 17403)" Thanks. Bala S --

[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

, dopc or dppc? Thanks Bala S -- View this message in context: http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4930616.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http