From: Jie Shi (shijie0204_at_tamu.edu)
Date: Sun Sep 11 2022 - 19:55:38 CDT
Hi Jeff,
It looks to me like you are doing everything right. I’ve run a lot of
membrane simulations based on CHARMM-GUI structures and have never seen
anything similar.
Yeah.. We have tried out all the possible things we can think of and still
have no idea how to solve this. Hopefully, we can find some new inputs here
from the NAMD community.
How long does it take the curvature to appear? Have you tried running
longer to see if the curvature disappears?
It usually took 3-10 ns for the curvature to appear. I have extended the
simulation to slightly over 100 ns, but the curvature stays throughout the
simulation.
Best,
Jie
On Sun, Sep 11, 2022 at 1:38 PM Jeff Comer <jeffcomer_at_gmail.com> wrote:
> It looks to me like you are doing everything right. I’ve run a lot of
> membrane simulations based on CHARMM-GUI structures and have never seen
> anything similar. How long does it take the curvature to appear? Have you
> tried running longer to
> ZjQcmQRYFpfptBannerStart
> This Message Is From an External Sender
> This message came from outside your organization.
>
> ZjQcmQRYFpfptBannerEnd
> It looks to me like you are doing everything right. I’ve run a lot of
> membrane simulations based on CHARMM-GUI structures and have never seen
> anything similar. How long does it take the curvature to appear? Have you
> tried running longer to see if the curvature disappears?
>
> Jeff
>
> On Sun, Sep 11, 2022 at 10:42 Jie Shi <shijie0204_at_tamu.edu> wrote:
>
>> Dear all,
>>
>> I am attempting to run a simulation of a system containing both membrane
>> (POPC) and protein with NAMD 2.14 on HPC. However, I found the membrane
>> forms an irregular spontaneous bending. So I then tested it with a
>> membrane-only system (without the protein, so only the POPC bilayer, water,
>> and ions are included), and a similar bending is again shown up, which
>> suggests it’s not the protein that induces the bending in the membrane. The
>> snapshot showing the bending can be found here
>> https://urldefense.com/v3/__https://i.postimg.cc/hGJKG085/bending.png__;!!DZ3fjg!87bovgTn76Q2kOMcLh66vVOsomxNMVWjZR2SnBsRrCU-9YaMN5l-Sf91NkU_V0CER5-5-UzOj1k-HNmKSgoektY$
>> <https://urldefense.com/v3/__https://i.postimg.cc/hGJKG085/bending.png__;!!DZ3fjg!5TK-Tost5XQnSTwWQC2eFOZxPDxhKhmmmz9Py2_Cj9wc-lttu9PKsm2FqPpNA0omR5qXWvwXDAOZj19q0CvBX1E$>
>> .
>>
>> Then we move the membrane-only system to a local server and run the same
>> simulation. It is done with exactly the same input configuration files, and
>> the same input psf/pdb files. But on our local server, the bending never
>> happens.
>>
>> Another weird thing we noticed: we then also started running several more
>> membrane simulations with/without protein, and all simulations show this
>> kind of bending in the membrane if run on HPC. And in all cases, the
>> bending happens along the Y-axis. This makes us wonder if it is a
>> systematic problem.
>>
>> In summary, simulation on the local server: no irregular bending;
>> Simulation on HPC, bending appears very soon (within 10~ns) after the
>> harmonic restraints are removed ( those restraints are for the stages of
>> energy minimization and equilibrations).
>> We have never seen this issue before and we are wondering if it is
>> related to the version of NAMD and/or along with the HPC. Please let us
>> know if anyone else encounters a similar problem and if anyone knows how to
>> solve this issue. Thank you in advance!
>>
>> More detailed information about our system:
>> a) Total atom numbers: 127146
>> b) There are 200 lipids (POPC) in each leaflet.
>> c) System dimensions:
>>
>> cellBasisVector1 125.02 0.0 0.0
>> cellBasisVector2 0.0 127.08 0.0
>> cellBasisVector3 0.0 0.0 101.07
>> cellOrigin 0.0 0.0 0.0
>>
>> More detailed information about our HPC:
>> 1) It’s IBM Aimosx Cluster (NPL).
>> 2) 20-core 2.5 GHz Intel Xeon CPUs
>> 3) Each node has 8 NVIDIA Tesla V100 GPUs with 32 GiB HBM
>>
>> More detailed information about our input files:
>> 1) psf/pdb files are created by CHARMM GUI.
>> 2) Input configuration file for the production run is also attached at
>> the end.
>> 3) We also have tried using the input configuration files generated by
>> CHARMM GUI, it also leads to membrane bending if run on HPC.
>>
>> Our research progress has been stuck for ~1 month due to this issue,
>> please help us resolve it. Any suggestions would be greatly appreciated.
>> Thank you again!
>>
>> Best,
>> Jie
>>
>>
>> ============================
>>
>> #############################################################
>> ## ADJUSTABLE PARAMETERS ##
>> #############################################################
>>
>> structure step5_input.psf
>> coordinates step5_input.pdb
>> outputName popc_npt01
>>
>> set temperature 303.15
>>
>> # Continuing a job from the restart files
>> if {1} {
>> set inputname popc_eq5
>> binCoordinates $inputname.restart.coor
>> binVelocities $inputname.restart.vel ;# remove the "temperature"
>> entry if you use this!
>> extendedSystem $inputname.restart.xsc
>> }
>>
>> firsttimestep 0
>>
>>
>> #############################################################
>> ## SIMULATION PARAMETERS ##
>> #############################################################
>>
>> # Input
>> paraTypeCharmm on
>>
>> parameters toppar/par_all36m_prot.prm
>> parameters toppar/par_all36_na.prm
>> parameters toppar/par_all36_carb.prm
>> parameters toppar/par_all36_lipid.prm
>> parameters toppar/par_all36_cgenff.prm
>> parameters toppar/par_interface.prm
>> # parameters toppar/toppar_all36_moreions.str
>> parameters toppar/toppar_all36_nano_lig.str
>> parameters toppar/toppar_all36_nano_lig_patch.str
>> parameters toppar/toppar_all36_synthetic_polymer.str
>> parameters toppar/toppar_all36_synthetic_polymer_patch.str
>> parameters toppar/toppar_all36_polymer_solvent.str
>> parameters toppar/toppar_water_ions.str
>> parameters toppar/toppar_dum_noble_gases.str
>> parameters toppar/toppar_ions_won.str
>> parameters toppar/toppar_all36_prot_arg0.str
>> parameters toppar/toppar_all36_prot_c36m_d_aminoacids.str
>> parameters toppar/toppar_all36_prot_fluoro_alkanes.str
>> parameters toppar/toppar_all36_prot_heme.str
>> parameters toppar/toppar_all36_prot_na_combined.str
>> parameters toppar/toppar_all36_prot_retinol.str
>> parameters toppar/toppar_all36_prot_model.str
>> parameters toppar/toppar_all36_prot_modify_res.str
>> parameters toppar/toppar_all36_na_nad_ppi.str
>> parameters toppar/toppar_all36_na_rna_modified.str
>> parameters toppar/toppar_all36_lipid_sphingo.str
>> parameters toppar/toppar_all36_lipid_archaeal.str
>> parameters toppar/toppar_all36_lipid_bacterial.str
>> parameters toppar/toppar_all36_lipid_cardiolipin.str
>> parameters toppar/toppar_all36_lipid_cholesterol.str
>> parameters toppar/toppar_all36_lipid_dag.str
>> parameters toppar/toppar_all36_lipid_inositol.str
>> parameters toppar/toppar_all36_lipid_lnp.str
>> parameters toppar/toppar_all36_lipid_lps.str
>> parameters toppar/toppar_all36_lipid_mycobacterial.str
>> parameters toppar/toppar_all36_lipid_miscellaneous.str
>> parameters toppar/toppar_all36_lipid_model.str
>> parameters toppar/toppar_all36_lipid_prot.str
>> parameters toppar/toppar_all36_lipid_tag.str
>> parameters toppar/toppar_all36_lipid_yeast.str
>> parameters toppar/toppar_all36_lipid_hmmm.str
>> parameters toppar/toppar_all36_lipid_detergent.str
>> parameters toppar/toppar_all36_lipid_ether.str
>> parameters toppar/toppar_all36_carb_glycolipid.str
>> parameters toppar/toppar_all36_carb_glycopeptide.str
>> parameters toppar/toppar_all36_carb_imlab.str
>> parameters toppar/toppar_all36_label_spin.str
>> parameters toppar/toppar_all36_label_fluorophore.str
>>
>>
>> # NOTE: Do not set the initial velocity temperature if you
>> # have also specified a .vel restart file!
>> # temperature $temperature
>>
>>
>> # Periodic Boundary Conditions
>> # NOTE: Do not set the periodic cell basis if you have also
>> # specified an .xsc restart file!
>> if {0} {
>> cellBasisVector1 125.02 0.0 0.0
>> cellBasisVector2 0.0 127.08 0.0
>> cellBasisVector3 0.0 0.0 101.07
>> cellOrigin 0.0 0.0 0.0
>> }
>>
>> wrapAll on
>>
>>
>> # Force-Field Parameters
>> exclude scaled1-4
>> 1-4scaling 1.0
>> cutoff 12.0
>> switching on
>> vdwForceSwitching yes
>> switchdist 10.0
>> pairlistdist 16.0
>>
>>
>> # Integrator Parameters
>> timestep 2.0 ;# 2fs/step
>> rigidBonds all ;# needed for 2fs steps
>> nonbondedFreq 1
>> fullElectFrequency 2
>> stepspercycle 20
>>
>>
>> #PME (for full-system periodic electrostatics)
>> # values of 30, 32, 36, 40, 45, 48, 50, 54, 60, 64, 72, 75, 80, 81, 90,
>> 96, 100, 120, 128
>> if {1} {
>> PME yes
>> PMEInterpOrder 6; # interpolation order (spline
>> order 6 in charmm)
>> PMEGridSpacing 1.0; # maximum PME grid space /
>> used to calculate grid size
>> }
>>
>>
>> # Constant Temperature Control
>> langevin on ;# do langevin dynamics
>> langevinDamping 1 ;# damping coefficient (gamma) of 5/ps
>> langevinTemp $temperature
>>
>> # Constant Pressure Control (variable volume)
>> if {1} {
>> useGroupPressure yes ;# needed for 2fs steps
>> useFlexibleCell yes ;# no for water box, yes for membrane
>> useConstantRatio yes;
>>
>> langevinPiston on
>> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
>> langevinPistonPeriod 200.0
>> langevinPistonDecay 50.0
>> langevinPistonTemp $temperature
>> }
>>
>> restartfreq 10000 ;# 1000steps = every 2ps
>> dcdfreq 10000 ;# 2 ps
>> xstFreq 10000 ;# every 20ps
>> dcdUnitCell yes;
>> outputEnergies 10000
>> outputTiming 10000
>> #outputPressure 500
>>
>>
>> # Fixed Atoms Constraint (set PDB beta-column to 1)
>> if {0} {
>> fixedAtoms on
>> fixedAtomsFile prot.fix
>> fixedAtomsCol B
>> fixedAtomsForces on
>> margin 3
>> }
>>
>> #############################################################
>> ## EXTRA PARAMETERS ##
>> #############################################################
>>
>> # Put here any custom parameters that are specific to
>> # this job (e.g., SMD, TclForces, etc...)
>> if {0} {
>> constraints on
>> consexp 2
>> consref popc.eq.step5.pdb
>> conskfile popc.eq.step5.pdb
>> conskcol B
>> margin 3
>> }
>>
>> #############################################################
>> ## EXECUTION SCRIPT ##
>> #############################################################
>>
>> # minimize 8000
>> run 10000000 ;# 20 ns (2fs timestep)
>>
>> --
>
> –––––––––––––––––––––––––––––––––––———————
> Jeffrey Comer, PhD
> Associate Professor
> Department of Anatomy and Physiology
> Kansas State University
> Office: 334 Coles Hall
> Phone: 785-532-6311
> Website: https://urldefense.com/v3/__http://jeffcomer.us__;!!DZ3fjg!87bovgTn76Q2kOMcLh66vVOsomxNMVWjZR2SnBsRrCU-9YaMN5l-Sf91NkU_V0CER5-5-UzOj1k-HNmKXQEus74$
> <https://urldefense.com/v3/__http://jeffcomer.us__;!!KwNVnqRv!DKe2NXR9XfYlwZBxeEX0-yX0nNh5e4YtMUbBPdOqgxt3pI8ZR0mj4JC3MDEZcrgoyete7vD7dp9HHairLAOv38E$>
>
This archive was generated by hypermail 2.1.6 : Tue Dec 13 2022 - 14:32:44 CST