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 <vvcha...@gmail.com
<mailto:vvcha...@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 <lecie...@googlemail.com
<mailto:lecie...@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 <vvcha...@gmail.com
<mailto:vvcha...@gmail.com>> wrote:
>>
>> Either a tighter pressure coupling time...
>>
>>
>>
>>
>> On Wed, Jun 1, 2011 at 2:57 PM, Vitaly Chaban
<vvcha...@gmail.com <mailto:vvcha...@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)
>> >
>> --
>> gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
--
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
