[gmx-users] Re: Doubt regarding membrane protein in POPC bilayer

Pawan Kumar wrote: Respected Sir, Greetings from Pawan. Thanks for all your suggestions and help. The solvation is completed and the system is neutralized. The position restraint mdrun and final mdrun has worked out successfully without any warnings and errors this time. The structure after t

[gmx-users] Re: Doubt regarding membrane protein in POPC bilayer

Pawan Kumar wrote: Respected Sir, Greetings from Pawan. Thanks for all your kind help and suggestions. I will work on this and ask you if I have further doubts. Is it fine if I use the perl code given in wiki.gromacs.org/membrane-simulations for

Re: [gmx-users] Re: Doubt regarding membrane protein in POPC bilayer

On Tue, Mar 31, 2009 at 07:23:57AM -0400, Justin A. Lemkul wrote: > > Force fields have to be internally self-consistent, so using the parameters > from OPLS with Berger lipids will give spurious results. The only proper > combinations are Gromos/Berger or OPLS/converted Berger. as long as one

[gmx-users] Re: Doubt regarding membrane protein in POPC bilayer

Pawan Kumar wrote: Respected Sir, Greetings from Pawan. I have edited the lipid.itp file to add just one line extra " H atom from the opls_force_filed.itp " at the end of lipid interactions data and that works fine. I have done this after seeing the archives. It was given either I should ch

[gmx-users] Re: Doubt regarding membrane protein in POPC bilayer

Justin A. Lemkul wrote: Pawan Kumar wrote: Respected Sir, Greetings from Pawan. I have used force constants of 10 in position restraint .itp files for proteins as suggested in Dr. Tieleman' s webisite for Inflategro. The mdp files are : The .mdp files look reasonable enough, althoug

[gmx-users] Re: Doubt regarding membrane protein in POPC bilayer

Pawan Kumar wrote: Respected Sir, Greetings from Pawan. I have used force constants of 10 in position restraint .itp files for proteins as suggested in Dr. Tieleman' s webisite for Inflategro. The mdp files are : The .mdp files look reasonable enough, although I don't know why you are

[gmx-users] Re: Doubt regarding membrane protein in POPC bilayer

Pawan Kumar wrote: Respected Sir, Greetings from Pawan. I did the Inflategro procedure for the POPC bilayer generated using genconf. It took around 26 compressions for coming near the initial area (just above it). The minimization were all converged to Fmax < 1350. If I decrease the Fmax les

[gmx-users] Re: Doubt regarding membrane protein in POPC bilayer

Pawan Kumar wrote: Respected Sir, Greetings from Pawan. I read in the manual about the freeze-grps but dint find a good explanation about the usage. Can you please tell me how to use freeze-grps in all dimensions during the minimizations ? If you search for "freezegrps" within the list

[gmx-users] Re: Doubt regarding membrane protein in POPC bilayer

Respected Sir, Thanks for all your help. I will try this out and if I have any further queries I will ask you. Thanks a lot. Thanking you, Pawan On Mon, Mar 23, 2009 at 5:58 PM, Justin A. Lemkul wrote: Pawan Kumar wrote: > Respected Sir, > > Thanks for all your help, suggestions and guidance

[gmx-users] Re: Doubt regarding membrane protein in POPC bilayer

Pawan Kumar wrote: Respected Sir, Thanks for all your help, suggestions and guidance. I have few more queries. Which type of box is appropriate in editconf - cubic or triclinic ? That depends entirely upon the dimensions of your system and what is adequate to accommodate the size of your em

[gmx-users] Re: Doubt regarding membrane protein in POPC bilayer

Pawan Kumar wrote: Respected Sir, Greetings from Pawan. Thanks for your reply. I used to do genbox first and then Inflategro all the time. Is it possible to concatenate one file after the other using " vi editor" - I mean just copying the contents of the membrane.gro file at the end of prote

[gmx-users] Re: Doubt regarding membrane protein in POPC bilayer

Pawan Kumar wrote: Respected Sir, Greetings from Pawan. Thanks for your mail. I will tell you in detail. The control lipid bilayer ( which is generated using genconf -nbox 2 2 1 -dist 0 0 0 ) minimized fine with an emtol value of 1510. Then after inserting the protein with genbox the whole sy

[gmx-users] Re: Doubt regarding membrane protein in POPC bilayer

Pawan Kumar wrote: Hello Justin Sir, Greetings from Pawan. Sorry for the inconvenience. Next time I will keep in mind about the subject line. I tried deleting those particular atoms where it gave the maximum force. You said that this atom was part of a lipid. Deleting these atoms will give