[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-URL-tp4930034p4957017.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)
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 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 -- View this message in context: http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4933137.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)
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 should I be using? I am using the usual command I use for non-membrane simulations, $ editconf -f shrinked4.gro -o shrinked4_1.gro -c -d 1 -bt cubic followed by $ genbox -cp shrinked4_1.gro -cs -o shrinked4_box.gro -p topol.top calculation goes for long time showing a huge number of 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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)
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. $ editconf -f shrinked4.gro -o shrinked4_1.gro -box 6.41840 6.44350 6.59650 $ genbox -cp shrinked4_1.gro -cs -o shrinked4_box.gro -p topol.top But I could see in the visualizer that SOL molecules were added on top and bottom but only 1/3 of the length of the bilayer. How to add SOL molecules 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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[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 question that how many iterations I should perform with inflateGRO program and what is the basis to stop and move with solvation step? Justin's one says that he could reach ~72 Å2 (which is above the expt. value ~62Å2). But when I am exactly following the tutorial with same KALP peptide. I am ending up with 'Area per lipid: 3.73355898918962 nm^2' within 10 iterations which is far lower than Justin's. Why? Thanks. -- View this message in context: http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4933801.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)
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 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.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)
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 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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[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 list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[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://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4934356.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[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 -- View this message in context: http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4934436.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)
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, 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://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
