[gmx-users] Potential Energy = -nan

hi i m doing simulation membrane protein while scaling down the lipids by a factor of 0.95 then performing EM Steepest Descents converged to Fmax 10 in 18 steps Potential Energy = -nan Maximum force = 4.7791553e+02 on atom 5440 Norm of force = -nan ; minim.mdp - used as input

[gmx-users] Potential Energy = -nan

hi I m using gromacs4.5.3 . hardware 1GB ram 320 hard disk . when i skiped scaling by factor 0.95 then , after EM step I m getting same potential energy nan result. i m doing simulation membrane protein while scaling down the lipids by a factor of 0.95 then performing EM Steepest

[gmx-users] Potential Energy = -nan

hi I m using gromacs4.5.3 . hardware 1GB ram 320 hard disk . Intel 32. I can perform simple task . I m trying nstxout=1 in my .mdp file. I will report u later. What is the hardware type? PowerPC, Intel 32- or 64-bit, etc? when i skiped scaling by factor 0.95 then , after EM step I m

[gmx-users] Potential Energy = -nan

hi, I m tried nstxout=1 in my .mdp file. Potential Energy = -nan Maximum force = 3.5637456e+07 on atom 2455 Norm of force = -nan help me! regards: shikha -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] Potential Energy = -nan

hi, I tried on other system , 4GB ram , core i3 ,64bit processor ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 10.0

[gmx-users] No such moleculetype NA+

hello , this is my ions.itp file for gromos53a6 forcefield [ moleculetype ] ; molnamenrexcl CU11 [ atoms ] ; idat typeres nr residu nameat name cg nrcharge mass 1CU1+1CU1CU 11 63.54600 [ moleculetype ] ; molnamenrexcl CU

[gmx-users] number of coordinates in coordinate file does not match topology

hello I m unable to update the [ molecules ] directive of topol_pope.top . grompp -f minim.mdp -c system_inflated.gro -p topol_pope.top -o em1.tpr Fatal error: number of coordinates in coordinate file (system_inflated.gro, 20782) does not match topology (topol_pope.top, 37867)

[gmx-users] generate .top file

hello Merry Christmas. this is my topol_pope.top file ; Include chain topologies #include forcefield.itp #include pope.itp ; Include water topology #include spc.itp ; Include ion topologies #include ions.itp ; System specifications [ system ] 340-Lipid POPE Bilayer [ molecules ] ;

[gmx-users] Illegal division by zero at inflategro

Hi I am having a trouble during inflategro scaling my system.gro perl inflategro system.gro 4 POPE 14 system_inflated.gro 5 area.dat Reading. Scaling lipids There are 0 lipids... Illegal division by zero at inflategro line 300. regards: shikha -- gmx-users

[gmx-users] reading tpx file version 73 with version 58 program

hi , Mr. justin thanx a lot for ur help! now i m able to generate system_inflated.gro. but while i m performing Run energy minimization accorning to tutorial getting this error grompp -f minim.mdp -c pope.gro -p topol_pope.top -o em1.tpr mdrun -v -s em1 -o em1 -c after_em -g emlog Fatal

[gmx-users] simulation of membrane protein

I am beginner in the GROMACS I am trying to simulate a theorical model of a membrane protein in explicit lipid bilayer membrane environment (DMPC or POPC), I have the pdb files of this protein and membrane , I have to topolies files this lipids (dmpc.ip or popc.itp). How we can create merged

[gmx-users] simulation of membrane protein

and protein and do simulation step by step. Anybody could help ? thank you very much ! with regards : shikha agarwal IIIT-A -- 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

[gmx-users] simulation of membrane protein

: /Program grompp, VERSION 4.0.7 Source code file: ../../gromacs-4.0.7/src/kernel/grompp.c, line: 320/ /Fatal error: No molecules were defined in the system / help me. shikha agarwal IIIT-A -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] Atomtype OW not found

Atomtype OW not found help me ! with regards: shikha agarwal IIIT-A (bioinformatics) -- 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

[gmx-users] Unknown bond_atomtype MNH3

Hello Justin, Thank you for your reply. I modifed ffG53a6bn_lipid.itp [ atomtypes ] ;name mass charge ptype c6 c12 ; LO15.99940.000 A 2.36400e-03 1.59000e-06 ;carbonyl O, OPLS LOM15.99940.000 A 2.36400e-03 1.59000e-06 ;carboxyl O, OPLS LNL