[gmx-users] Re: compression to study pressure effect
Justin A. Lemkul
jalemkul at vt.edu
Fri Jun 3 04:40:55 CEST 2011
Elisabeth wrote:
> Hello Dr. Vitaly Chaban,
>
> Thank you. I asked a friend in our Dept. for help who is working on
> different aspects of the more or less similar system. The message below
> was sent on behalf of me. I apologize if I should not have done this. We
> thought maybe it does not matter under which name messages are sent on
> the gmx list and the idea of using mailing list is to share knowledge
> regardless of names. I hope this has not offended you and other users.
>
> I am also asking Justin to let me know if I have violated mailing list
> rules. I make sure this will not happen again.
>
http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette
Having others send information around haphazardly to different individuals and
from colleagues or aliases just slows down your overall progress, since we don't
know who's getting (or providing) what information, or if the discussions are
even connected. Keep everything on the list and reply directly to questions
posed to you with as much detail as you can.
It's also not a good idea for anyone to complain that "no one on the list could
help much." I had been trying to extract the necessary diagnostic information
from you, but perhaps not at the pace you'd like. Problems aren't solved
instantly, especially via email by people who have only a very vague idea of
what you're doing.
-Justin
> Thank you,
> Best regards,
>
>
> On 2 June 2011 21:03, Vitaly Chaban <vvchaban at gmail.com
> <mailto:vvchaban at gmail.com>> wrote:
>
> Hey Eli:
>
> What is the correlation observed between you and Moeed?
>
> I suppose you eventually compressed your system so much, that it
> became very distorted. Check your GRO file. I believe it is not
> healthy inside.
>
> Regards.
>
> Dr. Vitaly V. Chaban, Department of Chemistry
> University of Rochester, Rochester, New York 14627-0216
>
>
>
>
> On Thu, Jun 2, 2011 at 6:53 PM, Moeed <lecielll at googlemail.com
> <mailto:lecielll at googlemail.com>> wrote:
> > Dear Dr.Chaban,
> >
> > I am so sorry to send you this message. Thank you for your
> comments. I have
> > encountered a problem that no one on the list could help much. I
> am very
> > hopeful you can assist me especially because I have noticed you
> respond to
> > messages dealing with compression or NPT runs. I am really
> confused since I
> > have been using the same input files (gro. top and mdp) and have been
> > collecting without any problem. Since yesterday I am getting a
> weird message
> > that is printed continuously until I kill mdrun.
> >
> >
> > arning: Only triclinic boxes with the first vector parallel to
> the x-axis
> > and the second vector in the xy-plane are supported.
> > Box (3x3):
> > Box[ 0]={ nan, nan, nan}
> > Box[ 1]={ nan, nan, nan}
> > Box[ 2]={ nan, nan, nan}
> >
> > I have only polyethylene chains in my system. I really appreciate
> if you
> > could help me or could kindly take a very brief look at my
> system. I can
> > send you top and gro files. I assure you top file is generated
> properly. I
> > have done many runs using that. Please let me know if you are
> interested.
> >
> > I thank you so much
> >
> > Waiting for your reply.
> >
> > Best regards,
> > Eli.
> >
> >
> > ; Run control
> > integrator = md
> > dt = 0.002
> > nsteps = 1000000 ;5000
> > nstcomm = 100
> >
> > ; Output control
> > nstenergy = 100
> > nstxout = 100
> > nstvout = 0
> > nstfout = 0
> > nstlog = 1000
> > nstxtcout = 1000
> >
> > ; Neighbor searching
> > nstlist = 10
> > ns_type = grid
> >
> > ; Electrostatics/VdW
> > coulombtype = Shift
> > vdw-type = Shift
> > rcoulomb-switch = 0
> > rvdw-switch = 0.9 ;0
> >
> > ; Cut-offs
> > rlist = 1.25
> > rcoulomb = 1.0 ;1.1
> > rvdw = 1.0
> >
> > ; Temperature coupling
> > Tcoupl = v-rescale
> > tc-grps = System ;HEX
> > tau_t = 0.1 ;0.1
> > ref_t = 300 ;300
> >
> > ; Pressure coupling
> > Pcoupl = Parrinello-Rahman
> > Pcoupltype = isotropic
> > tau_p = 1 ;0.5
> > compressibility = 4.5e-5 4.5e-5
> > ref_p = 10 30
> >
> > ; Velocity generation
> > gen_vel = yes
> > gen_temp = 300.0
> > gen_seed = 173529
> >
> > ; Bonds
> > constraints = all-bonds
> > constraint-algorithm = lincs
> >
> >
> >
> >
> >
> >
> > On 1 June 2011 14:59, Vitaly Chaban <vvchaban at gmail.com
> <mailto:vvchaban at gmail.com>> wrote:
> >>
> >> Either a tighter pressure coupling time...
> >>
> >>
> >>
> >>
> >> On Wed, Jun 1, 2011 at 2:57 PM, Vitaly Chaban
> <vvchaban at gmail.com <mailto:vvchaban at gmail.com>> wrote:
> >> > Hmm...
> >> >
> >> >
> >> > 1. The background of the task is not quite clear for me.
> >> >
> >> > 2. Evidently, the fluctuations are higher than the difference
> for your
> >> > pressures.
> >> >
> >> > 3. Why not to use significantly larger systems and significantly
> >> > larger difference between pressures?
> >> >
> >> >
> >> >
> >> > --
> >> > Dr. Vitaly V. Chaban, Department of Chemistry
> >> > University of Rochester, Rochester, New York 14627-0216
> >> >
> >> >
> >> >
> >> >
> >> >>
> >> >> I am trying to study the effect of pressure on total
> potential of my
> >> >> system
> >> >> (8 polymer chains). My problem is that I dont see a
> systematic effect
> >> >> of
> >> >> pressure on potentials and I cant judge if different
> pressures increase
> >> >> or
> >> >> decrease potential. This is the critical observable in my
> system and
> >> >> with
> >> >> high fluctuations I am getting I cant make comment on
> pressure effect.
> >> >> Total
> >> >> drift is high in most potential functions..I start my runs
> from a frame
> >> >> which is the output of an older NPT run (I use cpt file) that
> has a
> >> >> close
> >> >> density to what I want. In the production runs (NPT for 12 27
> 70 bar).
> >> >>
> >> >> Below is the settings I am using and I really appreciate it
> if you
> >> >> could
> >> >> comment on the most important factors for such a study. I tried
> >> >> different
> >> >> cutoffs as well...I though maybe increasing cutoffs invloves more
> >> >> interactions and can represent better the pressure effect...
> >> >>
> >> >> Thanks so much!
> >> >>
> >> >>
> >> >> ; Run control
> >> >> integrator = md
> >> >> dt = 0.002
> >> >> nsteps = 1000000 ;5000
> >> >> nstcomm = 100
> >> >>
> >> >> ; Output control
> >> >> nstenergy = 100
> >> >> nstxout = 100
> >> >> nstvout = 0
> >> >> nstfout = 0
> >> >> nstlog = 1000
> >> >> nstxtcout = 1000
> >> >>
> >> >> ; Neighbor searching
> >> >> nstlist = 10
> >> >> ns_type = grid
> >> >>
> >> >> ; Electrostatics/VdW
> >> >> coulombtype = Shift
> >> >> vdw-type = Shift
> >> >> rcoulomb-switch = 0.5 ;0
> >> >> rvdw-switch = 0.9 ;0
> >> >>
> >> >> ; Cut-offs
> >> >> rlist = 1.32 ;1.25 ; tired
> >> >> different
> >> >> cutoffs and r -switch...
> >> >> rcoulomb = 1.1 ;1.0
> >> >> rvdw = 1.1 ;1.0
> >> >>
> >> >> ; Temperature coupling
> >> >> Tcoupl = v-rescale
> >> >> tc-grps = System
> >> >> tau_t = 0.1
> >> >> ref_t = 300
> >> >>
> >> >> ; Pressure coupling
> >> >> Pcoupl = Parrinello-Rahman
> >> >> Pcoupltype = isotropic
> >> >> tau_p = 1
> >> >> compressibility = 3.5e-5
> >> >> ref_p = 10
> >> >>
> >> >> ; Velocity generation
> >> >> gen_vel = no;yes
> >> >> gen_temp = 300.0
> >> >> gen_seed = 173529
> >> >>
> >> >> ; Bonds
> >> >>
> >> >> constraints = all-bonds
> >> >> constraint-algorithm = lincs
> >> >>
> >> >>
> >> >> results for 12 27 70 bar resp.
> >> >>
> >> >>
> >> >> Statistics over 2043101 steps [ 500.0000 through 4586.2000 ps
> ], 17
> >> >> data
> >> >> sets
> >> >>
> >> >> All statistics are over 204311 points
> >> >>
> >> >>
> >> >>
> >> >> Energy Average Err.Est. RMSD
> Tot-Drift
> >> >>
> >> >>
> >> >>
> -------------------------------------------------------------------------------
> >> >>
> >> >> LJ (SR) -634.358 2.9 11.0696
> -20.3551
> >> >> (kJ/mol)
> >> >>
> >> >> Coulomb (SR) 184.082 1.4 3.62712
> 9.04046
> >> >> (kJ/mol)
> >> >>
> >> >> P*otential 642.528 6.4 23.1897
> -44.6636
> >> >> (kJ/mol)*
> >> >>
> >> >> Kinetic En. 904.294 0.075 16.2742
> 0.382223
> >> >> (kJ/mol)
> >> >>
> >> >> Total Energy 1546.82 6.3 28.6865
> -44.2813
> >> >> (kJ/mol)
> >> >>
> >> >> Temperature 300.186 0.025 5.4023
> 0.126881
> >> >> (K)
> >> >>
> >> >> Pressure 12.3856 0.89 887.501
> 5.41599
> >> >> (bar)
> >> >>
> >> >> Density 824.417 2.1 9.27838
> 14.7965
> >> >> (kg/m^3)
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >> Statistics over 750001 steps [ 500.0000 through 2000.0000 ps
> ], 17 data
> >> >> sets
> >> >>
> >> >> All statistics are over 75001 points
> >> >>
> >> >>
> >> >>
> >> >> Energy Average Err.Est. RMSD
> Tot-Drift
> >> >>
> >> >>
> >> >>
> -------------------------------------------------------------------------------
> >> >>
> >> >> LJ (SR) -638.643 4.3 12.0718
> -10.2094
> >> >> (kJ/mol)
> >> >>
> >> >> Coulomb (SR) 184.51 1 2.89777
> 5.99117
> >> >> (kJ/mol)
> >> >>
> >> >> *Potential 634.902 5.7 22.2857
> -21.4761
> >> >> (kJ/mol)*
> >> >>
> >> >> Kinetic En. 904.181 0.11 16.2261
> -0.275076
> >> >> (kJ/mol)
> >> >>
> >> >> Total Energy 1539.08 5.7 27.9661
> -21.7511
> >> >> (kJ/mol)
> >> >>
> >> >> Temperature 300.148 0.035 5.38636
> -0.0913135
> >> >> (K)
> >> >>
> >> >> Pressure 27.6467 1.4 881.409
> 8.58275
> >> >> (bar)
> >> >>
> >> >> Density 826.734 3.4 9.76089
> 6.06824
> >> >> (kg/m^3)
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >> 70 bar run
> >> >>
> >> >>
> >> >> even 6 ns runs gives large total drifts..e.g.13.4934 for
> density..
> >> >>
> >> >>
> >> >>
> >> >> Statistics over 2750001 steps [ 500.0000 through 6000.0000 ps
> ], 17
> >> >> data
> >> >> sets
> >> >>
> >> >> All statistics are over 275001 points
> >> >>
> >> >>
> >> >>
> >> >> Energy Average Err.Est. RMSD
> Tot-Drift
> >> >>
> >> >>
> >> >>
> -------------------------------------------------------------------------------
> >> >>
> >> >> LJ (SR) -639.206 3.7 11.6741
> -23.7773
> >> >> (kJ/mol)
> >> >>
> >> >> Coulomb (SR) 182.97 1.7 4.18663
> 11.8694
> >> >> (kJ/mol)
> >> >>
> >> >> *Potential 640.114 7.5 24.9191
> -51.8187
> >> >> (kJ/mol)*
> >> >>
> >> >> Kinetic En. 904.3 0.074 16.2887
> 0.161695
> >> >> (kJ/mol)
> >> >>
> >> >> Total Energy 1544.41 7.5 30.1347
> -51.657
> >> >> (kJ/mol)
> >> >>
> >> >> Temperature 300.187 0.024 5.40713
> 0.0536754
> >> >> (K)
> >> >>
> >> >> Pressure 69.7658 0.86 893.933
> -2.29885
> >> >> (bar)
> >> >>
> >> >> Density 829.657 2.3 8.98849
> 13.4934
> >> >> (kg/m^3)
> >> >
> >> --
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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