[nursya]

Good Day,

By any chance in the future, will genesis support simulation resume if the run crashed (especially at log7) just like gromacs capable doing that?

Again, system crashed and unexpected shutdown at 3am probably because of overheated..

Nur

[nursya]

Power supply suddenly off  in the area where i run this md simulation. However since i run this via ubuntu, they have optioj resume. BUT, i noticed only rst file update the time but not dcd and log 7 in this 2 hours after resume. I am not sure is this working or not. Should i just give up and run new?

[nursya]

I encountered error at this step in the RDF Analysis but the PDB that i used in the input was just the same PDB for simulation, area per lipid, and RMSD analysis which was a success. May I know why?

STEP3] Set Relevant Variables and Structures

Read_Psf> Summary of Psffile
psftype = xplor
num_atoms = 62627 num_bonds = 62982
num_angles = 67194 num_dihedrals = 85052
num_impropers = 440 num_cmap_terms = 0
num_HB_donors = 22276 num_HB_acceptors= 11138
num_NB_exclusion= 0 num_groups = 18923
total_charge = -0.000

Check_Pdb> 6-column residue sequence number

Define_Molecules> coordinates are not present. rank_no = 3

Hope can clear things out!

Thanks

[nursya]

good news. they already fixed the bugs(charmm-gui developer). i notice the new one resname was just: (rnam:ECLIPA and (an:PA)). they removed sid:MEMB and those empty bracket.

thanks for this nice discussion Dr Jung! i appreciate it

[nursya]

Hi

Tried that before, the error state:
Setup_Enefunc_Rest_Group> no atom in group rank_no = 1
Setup_Enefunc_Rest_Group> no atom in group rank_no = 0

Guess need to fill in that empty bracket resname also..

ECLIPA is E.coli lipid a type 1.
Another 2 parts of E. coli LPS need to mentioned I think, the core and the o-antigen. Mine is LPS type 1, R3, O55. But I dont know the resname for this R3 and O55..

[nursya]

i did not change anything from charmm-gui downloaded files.

i am suspecting the step6.0_minimization.inp files for this LPS is incomplete. because:
[SELECTION]
group1 = sid:MEMB and ((rnam: and ()) or (rnam: ECLIPA and (an:PA)))

remember the error notes that i wrote in Log6.0 is:
Select_atam> Syntax error. brakcet slis empty rank_no = 0

while the input files that i successfully run, POPC (step6.0_minimization.inp) that site read:
[SELECTION]
group1 =sid:MEMB and ((rnam:POPC and (an:P)))

differences you can see now is there is empty space in the bracket for inp file LPS(step6.0_minimization)

I tried to find what that script is, maybe ECR3O55 but still error after i fill that in (ECR3O55: e.coli R3, o55) as ECLIPA is the resname for e.coli type 1 Lipid A.

Hope for your help to figure this things out

[nursya]

Dear Jwjung,

This is how i do it..

^{export OMP_NUM_THREADS=1}

mpirun -np 1 home/ubuntu/Downloads/genesis-1.4.0/bin/spdyn step6.0_minimization.inp > log6.0

As from charmm-gui, i chose no of lipid: LPS upperleaflet 7 lowerleaflet 7. At first i am suspecting the size of LPS could be too big, innitially did tried 22 upper and 22 lower before decreasing it to 7.

then i chose 0.25M CaCl2, genesis, genesis, 303.15 and monte carlo

Perhaps the ‘language’ input created by charmm-gui for LPS cannot be read by Genesis-1.4.0?

[nursya]

do you mean path input of step5 generated by charmm-gui?