Re: [gmx-users] (no subject)

thank you very much sir. regards Suriyanarayanan On Sat, Aug 23, 2014 at 12:06 AM, Tsjerk Wassenaar wrote: > Hi Suriyanarayanan, > > You can check out the WeNMR Gromacs portal. > > Hope it helps, > > Tsjerk > On Aug 22, 2014 10:29 AM, "Balasubramanian Suriyanar

[gmx-users] (no subject)

Dear Users, generally for running a 10 ns simulation is there any online server facility available. This will be helpful for people who do not have a "continuous access" to the server. regards Suriyanarayanan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/

[gmx-users] (no subject)

Dear All, How can we decode the md.xtc or md.tpr files. Can it be opened in word file. regards Suri -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Maili

Re: [gmx-users] Energy minimisation step in Lipid protein simulation

e: > > > On 6/12/14, 4:54 AM, Balasubramanian Suriyanarayanan wrote: > >> Dear friends, In protein lipid simulation , when I do energy minimisation >> ster I get an error as " Ek! No confout.gro at all! >> >> Died at inflategro.pl line 10

[gmx-users] (no subject)

Dear friends, In protein lipid simulation , when I do energy minimisation ster I get an error as " Ek! No confout.gro at all! Died at inflategro.pl line 104." What is "confout.gro". If am right it is the output file that we get from the minimisation step. I used the command "

[gmx-users] energy minimisation in lipid protein simulation

Dear friends, In protein lipid simulation , when I do energy minimisation ster I get an error as " Ek! No confout.gro at all! Died at inflategro.pl line 104." What is "confout.gro". If am right it is the output file that we get from the minimisation step. I used the command "

[gmx-users] (no subject)

Why is my questions not appearing in the forum. Do I not follow the rules.' Please clarify. regards Suriyanarayanan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.

[gmx-users] energy minimisation step in protein lipid simulation

Dear friends, In protein lipid simulation , when I do energy minimisation ster I get an error as " Ek! No confout.gro at all! Died at inflategro.pl line 104." What is "confout.gro". If am right it is the output file that we get from the minimisation step. I used the command "

[gmx-users] energy minimisation step in lipid protein simulation

Dear friends, In protein lipid simulation , when I do energy minimisation ster I get an error as " Ek! No confout.gro at all! Died at inflategro.pl line 104." What is "confout.gro". If am right it is the output file that we get from the minimisation step. I used the command "

[gmx-users] Energy minimisation step in Lipid protein simulation

Dear friends, In protein lipid simulation , when I do energy minimisation ster I get an error as " Ek! No confout.gro at all! Died at inflategro.pl line 104." What is "confout.gro". If am right it is the output file that we get from the minimisation step. I used the command "

Re: [gmx-users] packing lipid around protein

e number of lipids removed from each > leaflet. > > Kind regards. > > Catarina A. Carvalheda dos Santos > > > On 10 June 2014 08:49, Balasubramanian Suriyanarayanan > wrote: > > > Dear Friends > > > > When I pack the lipids around the protein

[gmx-users] (no subject)

Dear Friends When I pack the lipids around the protein using the command "perl inflategro.pl system.gro 4 POPC 0 system_inflated.gro 5 area.dat", how do we know how many lipids are lost? regards, Suriyanarayanan -- Gromacs Users mailing list * Please search the archive at http://www.gromac

[gmx-users] packing lipid around protein

Dear Friends When I pack the lipids around the protein using the command "perl inflategro.pl system.gro 4 POPC 0 system_inflated.gro 5 area.dat", how do we know how many lipids are lost? regards Suriyanarayanan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.

Re: [gmx-users] (no subject)

al/justin/gmx-tutorials/membrane_protein/02_topology.html > > > On Tue, Jun 10, 2014 at 10:31 AM, Balasubramanian Suriyanarayanan < > bsns...@gmail.com> wrote: > > > Dear users, > > > > In a lipid membrane simulation " Grompp" command gives me a er

[gmx-users] Packing lipid around protein

Dear Friends When I pack the lipids around the protein using the command "perl inflategro.pl system.gro 4 POPC 0 system_inflated.gro 5 area.dat", how do we know how many lipids are lost? regards Suriyanarayanan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs

[gmx-users] (no subject)

Dear users, In a lipid membrane simulation " Grompp" command gives me a error " atom LC# not found". What do I need to change? regards Suriyanarayanan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * C

[gmx-users] NVT equilibration - error message

Thanks for your reply. when I create index file by grouping sol and ions, protein , ligand and lipid it works. But the next error message was "Group SOL_CL not found in indexfile. Maybe you have non-default goups in your .mdp file, while not using the '-n' option of grompp. In that case use the '

Re: [gmx-users] Problem in NVT equilibration

ly used "-n" option. regards Suriyanarayanan On Mon, Jun 9, 2014 at 3:00 PM, Venkat Reddy wrote: > Dear Surinarayanan, > You have to create appropriate index file by grouping solvent and solute > molecules separately (eg: Protein_ligand_membrane Water_and_ions). >

[gmx-users] Problem in NVT equilibration

Dear User I do a protein ligand simulation in a lipid environment. When I do NVT equilibration I get an error message saying "32 molecules are not part of any coupling groups". Do I need to change the .mdp file. Please clarify. Regards Surinarayanan -- Gromacs Users mailing list * Please se

[gmx-users] (no subject)

Dear users, Where can we get "gromos43a1.ff" from gromacs directory> please help me. regards Suriyanarayanan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Supp

[gmx-users] topol_pope.top

Dear Sir, If am using POPE model for simulation , where we have the access of p topol_pope.top. regards -- B.Suriyanarayanan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.

[gmx-users] membrane protein simulation - ligand introduction

Dear Users If membrane protein ligand complex needs to simulated in lipid bilayers then how to introduce ligand and at what step? regards -- B.Suriyanarayanan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posti

[gmx-users] Error: dangling bond at atleast one of terminals

Dear users, I am running membrane protein simulation in lipid environment. when I processed through pdb2gmx *pdb2gmx -f 3B5D.pdb -o 3B5D_processed.gro -ignh -ter -water spc* *I get the following out put and error. * *please n* *help* Select the Force Field: >From '/opt/bio/gromacs/share/gromac

[gmx-users] Protein preparation in Membrane simulation

Dear all When doing membrane simulation, do protein needs to be prepared in "Xleap module in Amber" as given in tutorials (Bevans Lab). regards -- B.Suriyanarayanan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

[gmx-users] (no subject)

Dear all In membrane protein simulation do we need to treat the Protein with lipid model with Leap module of AMBER before pdb2gmx step. what is the point in giving "none" option in response to -ter command. where we have capped N and C termini before pdb2gmx command? Please clarify. regards, -

[gmx-users] (no subject)

Dear all, I need to simulate a membrane protein (having transmembrane segments). what is the criteria in choosing LIPID MODELS such as DPPC, DOPC. regards, -- B.Suriyanarayanan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users