[gmx-users] Re: compression to study pressure effect
Vitaly Chaban
vvchaban at gmail.com
Fri Jun 3 03:03:00 CEST 2011
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> 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> wrote:
>>
>> Either a tighter pressure coupling time...
>>
>>
>>
>>
>> On Wed, Jun 1, 2011 at 2:57 PM, Vitaly Chaban <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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