Re: [gmx-users] Bilayer exploding with semiisotropic coupling
Hi,
I have added the energy minimization, npt and the final run log, edr and
mdp files in the drive folder. Here's the link again:
https://drive.google.com/drive/folders/1fUrx4yt3DpCEGY0CACA6n-PXcswfaa31?usp=sharing
I am prepping everything up to npt equilibration on my laptop. It has a
Intel i7-7820 HQ processor and a GEForce 940MX GPU. The production run is
done on another computer that has an Intel i7-8700K processor and a GTX
1080Ti and GTX 1060 GPUs. Both GPUs are used for the production run.
I use gmx mdrun -v -deffnm {filename} for the production run.
Hope these are helpful. Please let me know if any other information is
required.
Thank you
Namit
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Re: [gmx-users] Bilayer exploding with semiisotropic coupling
Hello, please upload the log file from the run, as well as the command you used to run the simulation and your system specs (processor, whether you are using GPUs). Then we can see what is wrong here. Thanks in advance. Cheers Paul On Sat, 4 Jan 2020, 21:14 Kevin Boyd, wrote: > Hi, > > Can you share more information? Please upload your starting configuration > and a log file. > > On Fri, Jan 3, 2020 at 10:29 AM Namit Chaudhary > wrote: > > > Hi, > > > > Sorry. I didn't realize that attachments aren't uploaded. Below is a link > > for the files mentioned in the original mail. > > > > > https://drive.google.com/drive/folders/1fUrx4yt3DpCEGY0CACA6n-PXcswfaa31?usp=sharing > > > > Namit > > > > On Fri, Jan 3, 2020 at 1:12 PM Namit Chaudhary > > wrote: > > > > > Hi all, > > > > > > I am trying to simulate a coarse grain system containing DPPC (10%), > > > Cholesterol (40%) and a custom lipid that's synthesized by our lab > (50%, > > > topology and martini mapping attached). Our lab uses these molecules > to > > > formulate lipid nanoparticles and deliver RNA therapeutics. I am trying > > to > > > understand the structure of these nanoparticles. I tried modelling them > > as > > > a bilayer but the system seems to be exploding in the z - direction > > during > > > the production run if I use semiisotropic or anisotropic pressure > > coupling > > > (isotropic coupling seems to work). Below is the md.mdp file that I am > > > using. > > > > > > integrator = md > > > dt = 0.01 > > > nsteps = 800 > > > nstcomm = 100 > > > comm-grps= LIPIDS SOL > > > > > > > > > nstxout = 0 > > > nstvout = 0 > > > nstfout = 0 > > > nstlog = 1000 ; Output frequency for energies to log > > > file > > > nstenergy= 100 ; Output frequency for energies to > > energy > > > file > > > nstxtcout= 1000 ; Output frequency for .xtc file > > > xtc_precision= 100 > > > xtc-grps = > > > energygrps = > > > > > > > > > nstlist = 10 > > > ns_type = grid > > > pbc = xyz > > > rlist= 1.1 > > > > > > coulombtype = reaction_field ;Reaction_field (for use > with > > > Verlet-pairlist) ;PME (especially with polarizable water) > > > rcoulomb_switch = 0.0 > > > rcoulomb = 1.1 > > > epsilon_r= 15 ; 2.5 (with polarizable water) > > > vdw_type = cutoff ;cutoff (for use with > Verlet-pairlist) > > > > > > rvdw_switch = 0.9 > > > rvdw = 1.1 ;1.1 (for use with Verlet-pairlist) > > > > > > cutoff-scheme= verlet > > > > > > tcoupl = v-rescale > > > tc-grps = LIPIDS SOL > > > tau_t = 1.0 1.0 > > > ref_t = 298 298 > > > Pcoupl = parrinello-rahman > > > Pcoupltype= semiisotropic > > > tau_p = 12.0 > > > compressibility = 3e-4 3e-4 ; 3e-4 > > > ref_p = 1.0 1.0 ; 1.0 1.0 > > > > > > gen_vel= yes > > > gen_temp = 298 > > > gen_seed = 473529 > > > > > > constraints= none > > > constraint_algorithm = Lincs > > > continuation = no > > > lincs_order= 4 > > > lincs_warnangle= 30 > > > > > > Is there something that I can change in my mdp file? Or is there > > something > > > wrong with the lipid itself? > > > > > > > > > Thank you > > > Namit > > > > > > > > > -- > > *Namit Chaudhary* > > Chemical Engineering | Carnegie Mellon University > > M: 724-506-0693 | E: nchau...@andrew.cmu.edu > > -- > > 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/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > 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/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- 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/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to
Re: [gmx-users] Bilayer exploding with semiisotropic coupling
Hi, Can you share more information? Please upload your starting configuration and a log file. On Fri, Jan 3, 2020 at 10:29 AM Namit Chaudhary wrote: > Hi, > > Sorry. I didn't realize that attachments aren't uploaded. Below is a link > for the files mentioned in the original mail. > > https://drive.google.com/drive/folders/1fUrx4yt3DpCEGY0CACA6n-PXcswfaa31?usp=sharing > > Namit > > On Fri, Jan 3, 2020 at 1:12 PM Namit Chaudhary > wrote: > > > Hi all, > > > > I am trying to simulate a coarse grain system containing DPPC (10%), > > Cholesterol (40%) and a custom lipid that's synthesized by our lab (50%, > > topology and martini mapping attached). Our lab uses these molecules to > > formulate lipid nanoparticles and deliver RNA therapeutics. I am trying > to > > understand the structure of these nanoparticles. I tried modelling them > as > > a bilayer but the system seems to be exploding in the z - direction > during > > the production run if I use semiisotropic or anisotropic pressure > coupling > > (isotropic coupling seems to work). Below is the md.mdp file that I am > > using. > > > > integrator = md > > dt = 0.01 > > nsteps = 800 > > nstcomm = 100 > > comm-grps= LIPIDS SOL > > > > > > nstxout = 0 > > nstvout = 0 > > nstfout = 0 > > nstlog = 1000 ; Output frequency for energies to log > > file > > nstenergy= 100 ; Output frequency for energies to > energy > > file > > nstxtcout= 1000 ; Output frequency for .xtc file > > xtc_precision= 100 > > xtc-grps = > > energygrps = > > > > > > nstlist = 10 > > ns_type = grid > > pbc = xyz > > rlist= 1.1 > > > > coulombtype = reaction_field ;Reaction_field (for use with > > Verlet-pairlist) ;PME (especially with polarizable water) > > rcoulomb_switch = 0.0 > > rcoulomb = 1.1 > > epsilon_r= 15 ; 2.5 (with polarizable water) > > vdw_type = cutoff ;cutoff (for use with Verlet-pairlist) > > > > rvdw_switch = 0.9 > > rvdw = 1.1 ;1.1 (for use with Verlet-pairlist) > > > > cutoff-scheme= verlet > > > > tcoupl = v-rescale > > tc-grps = LIPIDS SOL > > tau_t = 1.0 1.0 > > ref_t = 298 298 > > Pcoupl = parrinello-rahman > > Pcoupltype= semiisotropic > > tau_p = 12.0 > > compressibility = 3e-4 3e-4 ; 3e-4 > > ref_p = 1.0 1.0 ; 1.0 1.0 > > > > gen_vel= yes > > gen_temp = 298 > > gen_seed = 473529 > > > > constraints= none > > constraint_algorithm = Lincs > > continuation = no > > lincs_order= 4 > > lincs_warnangle= 30 > > > > Is there something that I can change in my mdp file? Or is there > something > > wrong with the lipid itself? > > > > > > Thank you > > Namit > > > > > -- > *Namit Chaudhary* > Chemical Engineering | Carnegie Mellon University > M: 724-506-0693 | E: nchau...@andrew.cmu.edu > -- > 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/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- 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/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Bilayer exploding with semiisotropic coupling
Hi, Sorry. I didn't realize that attachments aren't uploaded. Below is a link for the files mentioned in the original mail. https://drive.google.com/drive/folders/1fUrx4yt3DpCEGY0CACA6n-PXcswfaa31?usp=sharing Namit On Fri, Jan 3, 2020 at 1:12 PM Namit Chaudhary wrote: > Hi all, > > I am trying to simulate a coarse grain system containing DPPC (10%), > Cholesterol (40%) and a custom lipid that's synthesized by our lab (50%, > topology and martini mapping attached). Our lab uses these molecules to > formulate lipid nanoparticles and deliver RNA therapeutics. I am trying to > understand the structure of these nanoparticles. I tried modelling them as > a bilayer but the system seems to be exploding in the z - direction during > the production run if I use semiisotropic or anisotropic pressure coupling > (isotropic coupling seems to work). Below is the md.mdp file that I am > using. > > integrator = md > dt = 0.01 > nsteps = 800 > nstcomm = 100 > comm-grps= LIPIDS SOL > > > nstxout = 0 > nstvout = 0 > nstfout = 0 > nstlog = 1000 ; Output frequency for energies to log > file > nstenergy= 100 ; Output frequency for energies to energy > file > nstxtcout= 1000 ; Output frequency for .xtc file > xtc_precision= 100 > xtc-grps = > energygrps = > > > nstlist = 10 > ns_type = grid > pbc = xyz > rlist= 1.1 > > coulombtype = reaction_field ;Reaction_field (for use with > Verlet-pairlist) ;PME (especially with polarizable water) > rcoulomb_switch = 0.0 > rcoulomb = 1.1 > epsilon_r= 15 ; 2.5 (with polarizable water) > vdw_type = cutoff ;cutoff (for use with Verlet-pairlist) > > rvdw_switch = 0.9 > rvdw = 1.1 ;1.1 (for use with Verlet-pairlist) > > cutoff-scheme= verlet > > tcoupl = v-rescale > tc-grps = LIPIDS SOL > tau_t = 1.0 1.0 > ref_t = 298 298 > Pcoupl = parrinello-rahman > Pcoupltype= semiisotropic > tau_p = 12.0 > compressibility = 3e-4 3e-4 ; 3e-4 > ref_p = 1.0 1.0 ; 1.0 1.0 > > gen_vel= yes > gen_temp = 298 > gen_seed = 473529 > > constraints= none > constraint_algorithm = Lincs > continuation = no > lincs_order= 4 > lincs_warnangle= 30 > > Is there something that I can change in my mdp file? Or is there something > wrong with the lipid itself? > > > Thank you > Namit > -- *Namit Chaudhary* Chemical Engineering | Carnegie Mellon University M: 724-506-0693 | E: nchau...@andrew.cmu.edu -- 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/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
