VMD-L Mailing List

From: Luis Rosales (ludwig_at_correo.biomedicas.unam.mx)
Date: Wed Apr 20 2005 - 22:22:10 CDT

Hi all!
John,

Here is more concrete info on my problem,

I am using:

VMD for LINUX, version 1.8.3 (February 15, 2005) and NAMD 2.5 for
Tru64-Alpha-Elan (both precompiled binaries).

I run vmd on a local machine with 2 processors on RedHat Linux kernel
2.4.20-8smp and 4 Gb RAM
NAMD, on the other hand, is running on a remote alpha server SC45, true unix
5.1b, using 2 nodes (total 4 processors) with 2 Gb of RAM.

I ran this test on a system with 2 protein fragments and 0 waters, for a total
of 110 residues (1651 atoms). One protein is 85 residues long and the 2nd is
25 residues long.
In this case the simulation runs smoothly until I apply a force on the small
fragment:

------------------------------------
ENERGY: 115 142.9833 560.0360 549.5308 22.2029
       -2084.3060 -333.2643 0.0000 0.0000 257.1398
          -885.6774 52.2506 -886.1811 -885.7428 52.2506

ENERGY: 116 150.6783 545.7365 553.3336 22.7285
       -2088.9056 -333.2312 0.0000 0.0000 271.5344
          -878.1255 55.1756 -878.5663 -878.3913 55.1756

ENERGY: 117 152.8667 531.2275 557.0184 23.1223
       -2093.8173 -333.8267 0.0000 0.0000 290.1404
          -873.2688 58.9563 -873.2699 -874.7542 58.9563

ENERGY: 118 148.2011 516.6806 560.5185 23.1648
       -2099.0759 -335.1546 0.0000 0.0000 316.7026
          -868.9628 64.3537 -869.0747 -870.0510 64.3537

ENERGY: 119 141.9092 502.4293 563.7315 22.9768
       -2104.5040 -337.0257 0.0000 0.0000 348.3684
          -862.1145 70.7882 -862.8035 -861.5549 70.7882

ETITLE: TS BOND ANGLE DIHED IMPRP
            ELECT VDW BOUNDARY MISC KINETIC
              TOTAL TEMP TOTAL2 TOTAL3 TEMPAVG

ENERGY: 120 140.7723 488.7814 566.6368 22.7672
       -2110.2922 -339.3565 0.0000 0.0000 371.7358
          -858.9554 75.5364 -859.0029 -860.2378 75.5364

DEBUG: Detaching simulation from remote connection
ENERGY: 121 145.9771 475.7318 569.2369 22.4984
       -2116.4710 -341.5928 0.0000 0.0000 388.6565
          -855.9630 78.9747 -855.7663 -857.8394 78.9747

prun: ../namd/NAMD_2.5_Tru64-Alpha-Elan/namd2 (host bakliz8 process 1 pid
4857226) killed by signal 8 (FPE)
prun: no core file for job 30792 in /local/core/rms/30792
----------------------------------------

If I look over vmd I only can see:

Info) Connected to same-endian machine
Info) Using multithreaded IMD implementation.
Info) picked atom:
Info) ------------
Info) molecule id: 0
Info) name: HD1
Info) type: HD1
Info) index: 1499
Info) resname: TRP
Info) resid: 72
Info) chain: X
Info) segname: C
Info) x: 7.481662
Info) y: 2.785722
Info) z: 1.172789
Info) IMD connection ended unexpectedly; connection terminated.

**************************************************

On some cases, specially for the peptides approaching to the 15 residue limit,
 the message from NAMD is a little different, as if NAMD tried to pause the
simulation before quit: (this is the output for a system with a 85 residues
protein and a 16 residues peptide)

--------------------------------------
ENERGY: 146 174.5181 464.8836 526.1484 23.4186
       -2026.8350 -269.8708 0.0000 0.0000 381.4379
          -726.2993 84.9705 -725.8214 -727.5702 84.9705

ENERGY: 147 167.6455 468.3555 525.3417 23.7755
       -2026.7811 -270.8533 0.0000 0.0000 390.5575
          -721.9588 87.0020 -721.9038 -721.9578 87.0020

NAMD ABORTING DUE TO HARD NAMD_quit().
Info: Pausing IMD
prun: ../namd/NAMD_2.5_Tru64-Alpha-Elan/namd2 (host bakliz8 process 0 pid
4857107) killed by signal 11 (SEGV)
prun: no core file for job 30793 in /local/core/rms/30793
----------------------------------------

 As far as I can tell, the problem is not related to the duration of the
minimization, even with longer minimization runs, the process is killed when
the system enters the MD if I try to apply a force on a fragment longer than
15 residues, and usually the simulation is killed as soon as I click on the
fragment with my mouse....
[So, I dont have chance to exceed the speed of light... :( ]

So, in theory, there is a limit to the size of the fragment that I could
move/affect by aplying a reasonable force ?

Again, thanks for your time and help.

Kind regards,

Luis 

--
Open WebMail Project (http://openwebmail.org)
---------- Original Message -----------
From: John Stone <johns_at_ks.uiuc.edu>
To: Luis Rosales <ludwig_at_correo.biomedicas.unam.mx>
Cc: namd-l_at_ks.uiuc.edu, vmd-l_at_ks.uiuc.edu
Sent: Wed, 20 Apr 2005 16:12:20 -0500
Subject: namd-l: Re: vmd-l: Interactive Simulations, ligand size limits....
> Luis,
>   How large is the molecule you're simulating?  When you say that
> the simulation "crashed", does that mean that NAMD aborted because
> you pulled too hard (margin violation, exceeding the speed of light, 
> etc...), or did NAMD actually have a seg fault or floating point exception
> of some kind?   If you got a "margin violation" it means that you pulled
> on the structure so hard that you exceeded NAMD's internal limit on
> atom velocity imposed by the spatial decomposition it uses.  If you
> pull to hard and impart a tremendous velocity per simulated timestep,
>  this means that either you need to pull more gently, or you need to 
> decrease the gap in timescale between your real-time pulling and the 
> rate of simulated time in the simulation, either by using a smaller 
> molecule or by using fixed atoms, or some combination of both.
> 
>   John Stone
>   vmd_at_ks.uiuc.edu
> 
> -- 
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349         
>        WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078
------- End of Original Message -------