Re: [ESPResSo-users] Setting Up protein aggregation simulation

[Tristan Bereau]

Hi,

It's best if you notify everyone (address@hidden) when
the problem is solved.

Best,
Tristan


---------- Forwarded message ----------
From: Olujide Olubiyi <address@hidden>
Date: Mon, Jul 25, 2011 at 4:07 PM
Subject: Re: [ESPResSo-users] Setting Up protein aggregation simulation
To: Tristan Bereau <address@hidden>


Hello Tristan,

Thanks for your response. No, I didn't recompile Espresso after
uncommenting LJ_ANGLE.
I just did that now and it's working fine! Thanks a lot!

Jide Olu

On 07/25/11, Tristan Bereau  <address@hidden> wrote:

> Hi,
>
> Did you recompile Espresso after uncommenting the LJ_ANGLE feature in
> the myconfig.h file? It seems like that feature is not installed.
>
> Best,
> Tristan
>
> On Mon, Jul 25, 2011 at 3:33 PM, Olujide Olubiyi <address@hidden> wrote:
> > Dear users,
> >
> > I'm new to Espresso and I encountered the following error message while 
> > trying to run the input script(attached below):
> >
> >    ::peptideb::espresso > Error:  could not set interaction: 0 2 lj-angle 
> > 6.0 4.11 8. 1 -1 1 -2
> >    excessive parameter/unknown interaction type "lj-angle" in parsing non 
> > bonded interaction
> >
> > I tried uncommenting the appropriate sections of the myconfig.h file. A 
> > snapshot of this is:
> >
> > define TABULATED
> > define LENNARD_JONES
> > define SMOOTH_STEP
> > /* define BMHTF_NACL */
> > /* define LJ_WARN_WHEN_CLOSE */
> > /* define MORSE */
> >  define LJCOS
> > /* define LJCOS2 */
> > define LJ_ANGLE
> > define LENNARD_JONES_GENERIC
> >  define BUCKINGHAM
> > /* define SOFT_SPHERE */
> > /* define INTER_DPD */
> > /* define INTER_RF */
> >
> > /* Note: Activate ONLY ONE bonded
> > define BOND_ANGLE_HARMONIC
> >  define BOND_ANGLE_COSINE
> > /* #define BOND_ANGLE_COSSQUARE */
> >
> > I'm sure there are lot of things I'm likely to have done wrong, I will be 
> > grateful if anyone could point this out to me. I
> > used the command:
> >
> > Espresso peptidebuilder.tcl gnnqqny_15june_1.tcl -espresso
> >
> > And here is the content of the configuration file:
> >
> > set amino_acids {
> >    {GLY ASN ASN GLN GLN ASN TYR}
> >    {GLY ASN ASN GLN GLN ASN TYR}
> >    {GLY ASN ASN GLN GLN ASN TYR}
> >    {GLY ASN ASN GLN GLN ASN TYR}
> >    {GLY ASN ASN GLN GLN ASN TYR}
> >    {GLY ASN ASN GLN GLN ASN TYR}
> > }
> >
> > set display_O_H "on"
> >
> > set directory "gnnqqny_15june_1"
> > set PDB_file "$directory"
> > set filenumber 0
> >
> > set espresso_switch "on"
> >
> > set setbox_l {49.5 49.5 49.5}
> >
> > set warm_time_step 0.01
> > set main_time_step 0.01
> > set verlet_skin 0.4
> > set langevin_gamma 1.0
> > set systemtemp [expr 1.*$eps]
> > set charges "off"
> > set warm_steps 50
> > set warm_n_times 20
> > set int_steps 1000
> > set int_n_times 50000
> > set pdb_freq 10
> >
> > # Set the replica exchange temperatures
> > # 200 239 286 342 409 489 585 700 K
> > #set replica_temps { 0.67 0.80 1.00 1.15 1.37 1.64 1.96 2.35 }
> >
> > #200 217 233 250 267 283 300
> > set replica_temps { 0.63 0.68 0.73 0.78 0.82 0.86 0.89 0.91 0.93 0.95 0.98 
> > 1.01 1.06 1.12 1.17 1.22 }
> >
> > # number of times to integrate between each replica MC step
> > set replica_timestep 1000
> > # number of replica exchange rounds
> > set replica_rounds 500000
> > # frequency at which replica pdb files are written
> > set replica_pdb_freq 10
> >
> > Best regards,
> > Jide Olu
> > German Research School for Simulation Sciences,
> > Germany.
> >
> >