[gmx-users] Placing a peptide above aqueous phase of bilayer
Dear users, I want to place the peptide above aqueous phase of the bilayer.I have gone throught the mailing list and read the manual also, but since am a beginner to gromacs it will be very helpful if someone could mail me the commands to insert peptide above bilayer.I understood that it can be done with the combination of editconf and genbox.Please let me know the options to be included in these commands. -nikit ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] MD parameters for DPPC bilayer
dear users, Can anyone send me the Md parameters(.mdp file) for dppc molecule with 12lipids and 3655 water molecules that worked without any errors like "pressure scaling not more than 1%" and more?It will be very helpful as i will check out that with my mdp file. Thanks in advance ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] segmentation fault after mdrun
Dear justin, As you suggested i have changed the coloumb type to PME and set pme_order to 5 as said in the mailing list as it will increase the accuracy.But then the simulation is not getting completed.Its taking hours together.Normally what's the running time for a lipid bilayer?I dint find anything wrong with the topology as it is downloaded from tielman's website.it is also well equilibriated.Kindly give me your suggestions.My mdp.file is below: title= Yo cpp = cpp include = define = integrator = md tinit= 0 dt = 0.005 nsteps = 5 init_step= 0 comm-mode= Linear nstcomm = 1 comm-grps= system nstxout = 200 nstvout = 0 nstfout = 0 nstcheckpoint= 1000 nstlog = 100 nstenergy= 100 nstxtcout= 1000 xtc-precision= 1000 nstlist = 10 ns_type = grid pbc = xyz rlist= 1.0 domain-decomposition = no coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.0 epsilon-r= 1 vdw-type = Cut-off rvdw-switch = 0 rvdw = 1.0 DispCorr = EnerPres table-extension = 1 fourierspacing = 0.12 Pcoupl = berendsen Pcoupltype = semiisotropic tau_p= 0.5 0.5 0.5 compressibility = 4.5e-5 4.5e-5 4.5e-5 ref_p= 1.0 1.0 1.0 andersen_seed= 815131 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] segmentation fault after mdrun
Hello sir, Thanks for your suggestion.Then as u suggested i start the work from scratch and did the equilibriation again, there is nothing wrong with the topology also because it was taken from tiemann's website.The only message that it gives after equlibriation run is "Steepest Descents converged to machine precision in 159 steps, but did not reach the requested Fmax < 1e-05. Potential Energy = -3.3737231e+05 Maximum force = 2.6356035e+03 on atom 4665 Norm of force = 1.2290095e+04" do i have to upgrade to double precision for simuating dppc bilayer?but many of them worked fine with single precision alone. When i proceded with the production run, again either its not giving run with 5 steps or when i reduced step from 5 to 50 to check what's the output then it gives me an error saying " Warning: pressure scaling more than 1%, mu: 1.12479 1.12479 1.00476 Back Off! I just backed up step7018.pdb to ./#step7018.pdb.1# Wrote pdb files with previous and current coordinates Segmentation fault " since its giving an error with pressure scaling, the parameter that i need to adjust is ref_p??by default i said that to 1.0?Now what value i have to change. I willl be really thanful if you have a look at the segmentation fault also. title= Yo cpp = cpp include = define = integrator = md tinit= 0 dt = 0.005 nsteps = 5 init_step= 0 comm-mode= Linear nstcomm = 1 comm-grps= system nstxout = 200 nstvout = 0 nstfout = 0 nstcheckpoint= 1000 nstlog = 100 nstenergy= 100 nstxtcout= 1000 xtc-precision= 1000 nstlist = 10 ns_type = grid pbc = xyz rlist= 1.0 domain-decomposition = no coulombtype = Cut-off rcoulomb-switch = 0 rcoulomb = 1.0 epsilon-r= 1 vdw-type = Cut-off rvdw-switch = 0 rvdw = 1.0 DispCorr = EnerPres table-extension = 1 fourierspacing = 0.12 Pcoupl = berendsen Pcoupltype = semiisotropic tau_p= 0.5 0.5 0.5 compressibility = 4.5e-5 4.5e-5 4.5e-5 ref_p= 1.0 1.0 1.0 andersen_seed= 815131 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Error after Mdrun
Dear all, I need some help in my simulation. I Put system(dppc bilayer) in a cubic box then solvated it and made a equlibriation run.There were no issues till then.But when i proceded with the production run , the simulation crashes in no more than 5 or 10 steps leaving an error message saying , "Fatal error: Number of grid cells is zero. Probably the system and box collapsed" And there are warnings like: 1-4 interactions between 1163 and 1184 at distance 1.026 which is larger than the 1-4 table size 1 nm, This usually means your system is exploding. Warning: pressure scaling more than 1%, mu: 2.31762e+27 2.31762e+27 2.31762e+27 I tried to increase the table size but as I increased this value the distance always increased together, and I got again the same warning with different values, so this didn´t help. I tried energy minimization further but there also it ends up with "Steepest Descents converged to machine precision in 166 steps, but did not reach the requested Fmax < 1e-05. Potential Energy = -3.4207141e+05 Maximum force = 5.0177407e+03 on atom 5265 Norm of force = 1.3222472e+04 am getting the energy in a low negative value and also I have already gone through the mailing list regarding the same issue.But i couldn't get it clear. I am still a begginer in Gromacs, and I really don´t know what could bethe reason for these errors... It is also the first time that I am dealing with molecular dynamics simulation. Someone wrote me that it could besomething related to topologies, but i really couldn´t find where the error was. So I ask for your kindness help. Suggestions and advices will be welcome, i prod_NPT.mdp Description: Binary data ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
