From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Nov 05 2013 - 13:58:55 CST
I have fixed all said issues.
fp
On Tue, Nov 5, 2013 at 8:53 AM, Francesco Pietra <chiendarret_at_gmail.com>wrote:
> Sorry, a word was lacking (now in capital letters):
>
> on restarting by editing everything except the shared simulation options
>> (as in the example provided by namd, where, however, there were no
>> colvars), the new t-remd starts from the same INITIAL average conformation
>> of the peptide/protein as previous t-remd.
>>
>
> That is, I had expected that the new t-remd starts from where the previous
> t-remd ended.
>
> fp
>
> ---------- Forwarded message ----------
> From: Francesco Pietra <chiendarret_at_gmail.com>
> Date: Tue, Nov 5, 2013 at 8:48 AM
> Subject: Fwd: namd-l: Restarting T-REMD with colvars
> To: NAMD <namd-l_at_ks.uiuc.edu>
>
>
> To be clearer, on restarting by editing everything except the shared
> simulation options (as in the example provided by namd, where, however,
> there were no colvars), the new t-remd starts from the same average
> conformation of the peptide/protein as previous t-remd. That is my analysis
> from sorted simul at the same temperature.
>
> Hopefully I am wrong, otherwise the subsequent t-remd does not add to the
> previous one. Should my analysis be correct, it would be difficult for me
> to arrive at some kind of equilibration (no matter how you would like to
> define it) as the supercomputer use is limited to 24h batches. Which is far
> from what is needed for equilibration.
>
> I very much hope to be noticed of a wrong procedure (with, please, a
> correction as to carry out correctly a t-remd with rmsd colvars)
>
> cheers
> francesco pietra
>
>
> ---------- Forwarded message ----------
> From: Francesco Pietra <chiendarret_at_gmail.com>
> Date: Mon, Nov 4, 2013 at 5:19 PM
> Subject: namd-l: Restarting T-REMD with colvars
> To: NAMD <namd-l_at_ks.uiuc.edu>
>
>
> Hello:
> I wonder whether restarting a t-remd, particularly when colvars were
> imposed, goes straigth as indicated in the example of namd2.9 (or namd2.10,
> which I am currently using).
>
> That is, job1.conf (for the first restarting) reads
>
> *******************
> source fold_alanin.conf
> source [format $output_root.job0.restart10000.tcl ""]
> set num_runs 20000
>
> # prevent VMD from reading replica.namd by trying command only NAMD has
> if { ! [catch numPes] } { source ../replica.namd }
> *******************
>
> while the shared simulation options read:
>
> ************
> # shared simulation options for replica exchange
>
> timestep 1.0
>
> structure alanin.psf
> coordinates unfolded.pdb
>
> margin 10.0
> stepspercycle 100
> parameters alanin.params
> exclude scaled1-4
> 1-4scaling 0.4
> switching on
> switchdist 7.0
> cutoff 8.0
> pairlistdist 10.0
>
> langevin on
> langevinDamping 10.0
> *************
>
> I can imagine (hope) that job1 scipt lets the simulation taking the
> coordinates aftef execution of job0. However, what about if colvars were
> imposed? For example, my shared simulation options read:
>
> ********************
>
> # Shared simulation base and options
> # for parallel tempering
> # System P2i implicit NVT GB-SASA
>
> # forcefield
> paratypecharmm on
> parameters ./par_all27_prot_lipid.prm
>
> # molecules
> structure ./P2i.psf
> coordinates ./nvt-02.pdb
>
> # constraints
> colvars on ; # provide colvarsConfig (and colvarsINput if
> restart)
> colvarsConfig ./P2i_rmsd-colvars.in
> colvarsInput ./nvt-02.restart.colvars.state
>
> # about temperature
> langevin on
> langevinDamping 10.0
>
> # Approximations
> rigidBonds all ;# needed for 2fs/step
> rigidTolerance 0.000001
> exclude scaled1-4
> cutoff 18.0
> alphaCutoff 15.0 ;# for calc Born radii default 15.0
> 1-4scaling 1.0
>
> # GBIS parameters
> GBIS on
> switching on
> switchdist 15.0 ;# like in manual
> pairlistdist 18.0 ;# like in manual
> solventDielectric 80
> ionConcentration 0.15
> intrinsicRadiusOffset 0.09 ;# shrinks intrinsic atomic radii default 0.09
> GBISDelta 1.0 ;# calc Born radii default 1.0
> GBISBeta 0.8 ;# for cal Born radii default 0.8
> GBISGamma 4.85 ;# for calc Born radii default 4.85
>
> # Hydrophobic energy
> sasa on
> surfaceTension 0.006 ;# like in manual
>
> # Multistep integrator parameters
> timestep 2.0 ;# 2.0 fs/step
> nonbondedFreq 2 ;# nonbonded forces every two steps
> fullElectFrequency 4 ;# multiple of nonbondedFreq
> stepspercycle 20 ;# redo pairlist every 20 steps
>
> *******************
>
> My concern is at least related to the flag
>
> colvarsInput ./nvt-02.restart.colvars.state
>
>
> Is it correct to leave that unchanged on restarting? Actaully, all that
> above seems to work, also restarts, however, looking into what happens
> those issues above came out outstandingly. Given the cost of a 32-replica
> t-remd, I would like to understand it better.
>
> Very grateful for advice
>
> francesco pietra
>
>
>
>
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