[gmx-users] increasing cut-off and PME grid spacing

2011-08-21 Thread Hsin-Lin Chiang 
Hi Justin,

I understand now.
The vector of box changed from 5.8 to 44 after the short MD for equilibrium.
I don't know what happened during equilibrium.
But that is belong to the other question now.
Thank you very much for your reply.

Sincerely yours,
Hsin-LIn
 Hsin-Lin Chiang wrote: 
  Hi, Justin 
  
  Sorry for the unclear message. 
  My box vector in .gro file are 44.22834 #160;44.22834 #160;44.22834 and 
  the 
  number of atoms is 20171 
 
 You've set an unreasonably large box, as I expected. #160;The box should be 
 set in 
 nm, not Angstrom. #160;20171 atoms is a fairly small system, and in effect 
 what 
 you've created is a protein in a droplet of water, surrounded by vacuum. 
 #160;90% of 
 the work done by PME will be to calculate a grid of nothing. 
 
  The output of grompp is shown below, 
  I don't know if it is enough and I'm sorry I don't know how should I do 
  after you reply. 
  Could you please give me more messages in detail? 
 
 The solution is to set a correct box, unless your objective is to simulate a 
 droplet, in which case you have no choice but to take the performance loss 
 inherent to using PME. 
 
 -Justin

 
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[gmx-users] increasing cut-off and PME grid spacing

2011-08-20 Thread Hsin-Lin Chiang 
Hi,

I want to run mdrun -nt 12 on our cluster.

When I execute,
grompp -f test.mdp -o test.tpr -c ../3eq/eq.gro -t ../3eq/eq.trr -p 
../initial/insulin.top -n ../initial/index.ndx

I got the message,

Estimate for the relative computational load of the PME mesh part: 1.00

NOTE 1 [file test.mdp]:
#160; The optimal PME mesh load for parallel simulations is below 0.5
#160; and for highly parallel simulations between 0.25 and 0.33,
#160; for higher performance, increase the cut-off and the PME grid spacing

Then I changed my mdp to get

Estimate for the relative computational load of the PME mesh part: 0.20

Belos is my new mdp file
I change rlist, rcoulumb, and rvdw from 1 to 12 and fourierspacing from 0.2 to 
2 to get the lower relative computational load.
I'm afraid these extreme high value caused some bad effect.

title#160;#160;#160;#160;#160;#160;#160; = ttt
cpp#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
 =#160; /lib/cpp
constraints#160;#160;#160;#160;#160;#160;#160;#160; =#160; hbonds
;define#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
 =#160; -DFLEX_SPC
integrator#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; md
emtol#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
 =#160; 100.0
emstep#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
 =#160; 0.005
dt#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
 =#160; 0.002#160;#160;#160; ; ps !
nsteps#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
 =#160; 2500#160; ; total 50 ns
nstcomm#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; 
=#160; 5000
nstxout#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; 
=#160; 5000
nstvout#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; 
=#160; 5000
nstfout#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; 
=#160; 5000
nstlog#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
 =#160; 5000
nstenergy#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 
5000
nstlist#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; 
=#160; 10
ns_type#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; 
=#160; grid
rlist#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
 =#160; 12
rcoulomb#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; 
=#160; 12
rvdw#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
 =#160; 12
coulombtype#160;#160;#160;#160;#160;#160;#160;#160; =#160; PME
fourierspacing#160;#160;#160;#160;#160; =#160; 2
pme_order#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 6
optimize_fft#160;#160;#160;#160;#160;#160;#160; =#160; yes
Tcoupl#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
 =#160; v-rescale
tc-grps#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; 
=#160; Protein Non-Protein
;tau_t#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
 =#160; 0.1#160; 0.1
tau_t#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
 =#160; 0.2 0.2
ref_t#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
 =#160; 300 300
energygrps#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 
A-chain B-chain SOL NA
Pcoupl#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
 =#160; berendsen
Pcoupltype#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 
isotropic
;tau_p#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
 =#160; 0.1
tau_p#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
 =#160; 0.25
compressibility#160;#160;#160;#160; =#160; 5.4e-5
ref_p#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
 =#160; 1.0
gen_vel#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; 
=#160; yes
gen_temp#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; 
=#160; 300
gen_seed#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; 
=#160; 173529

Sincerely yours,
Hsin-Lin
 
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Re: [gmx-users] increasing cut-off and PME grid spacing

2011-08-20 Thread Justin A. Lemkul 



Hsin-Lin Chiang wrote:

**Hi,

I want to run mdrun -nt 12 on our cluster.

When I execute,
grompp -f test.mdp -o test.tpr -c ../3eq/eq.gro -t ../3eq/eq.trr -p 
../initial/insulin.top -n ../initial/index.ndx


I got the message,

Estimate for the relative computational load of the PME mesh part: 1.00

NOTE 1 [file test.mdp]:
  The optimal PME mesh load for parallel simulations is below 0.5
  and for highly parallel simulations between 0.25 and 0.33,
  for higher performance, increase the cut-off and the PME grid spacing


Then I changed my mdp to get

Estimate for the relative computational load of the PME mesh part: 0.20

Belos is my new mdp file
I change rlist, rcoulumb, and rvdw from 1 to 12 and fourierspacing from 
0.2 to 2 to get the lower relative computational load.

I'm afraid these extreme high value caused some bad effect.



If the simulation is even stable, it will be horribly inaccurate.  12 nm cutoffs 
are unheard of and 2-nm grid spacing is about 20 times too large.


Without seeing the original .mdp file that gave the high PME load, and without a 
further description about how large the system is (number of atoms), it is hard 
to say what you should do.  Some system do not parallelize well, but I imagine 
you should be able to get better performance.


-Justin


title= ttt
cpp =  /lib/cpp
constraints =  hbonds
;define  =  -DFLEX_SPC
integrator  =  md
emtol   =  100.0
emstep  =  0.005
dt  =  0.002; ps !
nsteps  =  2500  ; total 50 ns
nstcomm =  5000
nstxout =  5000
nstvout =  5000
nstfout =  5000
nstlog  =  5000
nstenergy   =  5000
nstlist =  10
ns_type =  grid
rlist   =  12
rcoulomb=  12
rvdw=  12
coulombtype =  PME
fourierspacing  =  2
pme_order   =  6
optimize_fft=  yes
Tcoupl  =  v-rescale
tc-grps =  Protein Non-Protein
;tau_t   =  0.1  0.1
tau_t   =  0.2 0.2
ref_t   =  300 300
energygrps  =  A-chain B-chain SOL NA
Pcoupl  =  berendsen
Pcoupltype  =  isotropic
;tau_p   =  0.1
tau_p   =  0.25
compressibility =  5.4e-5
ref_p   =  1.0
gen_vel =  yes
gen_temp=  300
gen_seed=  173529


Sincerely yours,
Hsin-Lin



--


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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[gmx-users] increasing cut-off and PME grid spacing

2011-08-20 Thread Hsin-Lin Chiang 
Sorry for the confusing symbol.

I tried to change it in this new mail.

Hi,

I want to run mdrun -nt 12 on our cluster.

When I execute,
grompp -f test.mdp -o test.tpr -c ../3eq/eq.gro -t ../3eq/eq.trr -p 
../initial/insulin.top -n ../initial/index.ndx

I got the message,

Estimate for the relative computational load of the PME mesh part: 1.00

NOTE 1 [file test.mdp]:
The optimal PME mesh load for parallel simulations is below 0.5
and for highly parallel simulations between 0.25 and 0.33,
for higher performance, increase the cut-off and the PME grid spacing

Then I changed my mdp to get

Estimate for the relative computational load of the PME mesh part: 0.20

Belos is my new mdp file
I change rlist, rcoulumb, and rvdw from 1 to 12 and fourierspacing from 0.2 to 
2 to get the lower relative computational load.
I'm afraid these extreme high value caused some bad effect.

title = ttt
cpp = /lib/cpp
constraints = hbonds
;define = -DFLEX_SPC
integrator = md
emtol = 100.0
emstep = 0.005
dt = 0.002 ; ps !
nsteps = 2500 ; total 50 ns
nstcomm = 5000
nstxout = 5000
nstvout = 5000
nstfout = 5000
nstlog = 5000
nstenergy = 5000
nstlist = 10
ns_type = grid
rlist = 12
rcoulomb = 12
rvdw = 12
coulombtype = PME
fourierspacing = 2
pme_order = 6
optimize_fft = yes
Tcoupl = v-rescale
tc-grps = Protein Non-Protein
;tau_t = 0.1 0.1
tau_t = 0.2 0.2
ref_t = 300 300
energygrps = A-chain B-chain SOL NA
Pcoupl = berendsen
Pcoupltype = isotropic
;tau_p = 0.1
tau_p = 0.25
compressibility = 5.4e-5
ref_p = 1.0
gen_vel = yes
gen_temp = 300
gen_seed = 173529

Sincerely yours,
Hsin-Lin 
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[gmx-users] increasing cut-off and PME grid spacing

2011-08-20 Thread Hsin-Lin Chiang 
If the simulation is even stable, it will be horribly inaccurate. 12 nm 
cutoffs 
are unheard of and 2-nm grid spacing is about 20 times too large.

Without seeing the original .mdp file that gave the high PME load, and without 
a 
further description about how large the system is (number of atoms), it is 
hard 
to say what you should do. Some system do not parallelize well, but I imagine 
you should be able to get better performance.

-Justin

Thank you for reply

The original .mdp is below and the number of atoms is 20171

The difference is only in rlist, rcoulomb, rvdw, and fourierspacing

title = ttt
cpp = /lib/cpp
constraints = hbonds
;define = -DFLEX_SPC
integrator = md
emtol = 100.0
emstep = 0.005
dt = 0.002 ; ps !
nsteps = 2500 ; total 50 ns
nstcomm = 5000
nstxout = 5000
nstvout = 5000
nstfout = 5000
nstlog = 5000
nstenergy = 5000
nstlist = 10
ns_type = grid

rlist = 1
rcoulomb = 1
rvdw = 1
coulombtype = PME
fourierspacing = 0.2
pme_order = 6
optimize_fft = yes
Tcoupl = v-rescale
tc-grps = Protein Non-Protein
;tau_t = 0.1 0.1
tau_t = 0.2 0.2
ref_t = 300 300
energygrps = A-chain B-chain SOL NA
Pcoupl = berendsen
Pcoupltype = isotropic
;tau_p = 0.1
tau_p = 0.25
compressibility = 5.4e-5
ref_p = 1.0
gen_vel = yes
gen_temp = 300
gen_seed = 173529

Hsin-Lin

 
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Re: [gmx-users] increasing cut-off and PME grid spacing

2011-08-20 Thread Justin A. Lemkul 



Hsin-Lin Chiang wrote:
If the simulation is even stable, it will be horribly inaccurate.  12 nm cutoffs 
are unheard of and 2-nm grid spacing is about 20 times too large.


Without seeing the original .mdp file that gave the high PME load, and without a 
further description about how large the system is (number of atoms), it is hard 
to say what you should do.  Some system do not parallelize well, but I imagine 
you should be able to get better performance.


-Justin




Thank you for reply

The original .mdp is below and the number of atoms is 20171



How big is the box?  You don't have any vacuum space, do you?  The only reason 
I've seen for PME load being so large in conjunction with normal settings and 
a simple system is if you've got a large void that causes PME to do a whole lot 
of work to accomplish nothing.


-Justin


The difference is only in rlist, rcoulomb, rvdw, and fourierspacing



/title= ttt
//cpp =  /lib/cpp
//constraints =  hbonds
//;define  =  -DFLEX_SPC
/i/ntegrator  =  md
//emtol   =  100.0
//emstep  =  0.005
//dt  =  0.002; ps !
//nsteps  =  2500  ; total 50 ns
//nstcomm =  5000
//nstxout =  5000
//nstvout =  5000
//nstfout =  5000
//nstlog  =  5000
//nstenergy   =  5000
//nstlist =  10
//ns_type =  grid

//rlist   =  1
//rcoulomb=  1
//rvdw=  1
//coulombtype =  PME
//fourierspacing  =  0.2
//pme_order   =  6
//optimize_fft=  yes
//Tcoupl  =  v-rescale
//tc-grps =  Protein Non-Protein
//;tau_t   =  0.1  0.1
//tau_t   =  0.2 0.2
//ref_t   =  300 300
//energygrps  =  A-chain B-chain SOL NA
//Pcoupl  =  berendsen
//Pcoupltype  =  isotropic
//;tau_p   =  0.1
//tau_p   =  0.25
//compressibility =  5.4e-5
//ref_p   =  1.0
//gen_vel =  yes
//gen_temp=  300
//gen_seed=  173529/



Hsin-Lin



--


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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[gmx-users] increasing cut-off and PME grid spacing

2011-08-20 Thread Hsin-Lin Chiang 
Hi, Justin

Sorry for the unclear message.
My box vector in .gro file are 44.22834#160; 44.22834#160; 44.22834 and the 
number of atoms is 20171
The output of grompp is shown below,
I don't know if it is enough and I'm sorry I don't know how should I do after 
you reply.
Could you please give me more messages in detail?

Hsin-Lin
---
#160;#160;#160;#160;#160;#160;#160; Written by Emile Apol, Rossen 
Apostolov, Herman J.C. Berendsen,
#160;#160;#160;#160;#160; Aldert van Buuren, P#228;r Bjelkmar, Rudi van 
Drunen, Anton Feenstra,
#160;#160;#160;#160;#160;#160;#160; Gerrit Groenhof, Peter Kasson, Per 
Larsson, Pieter Meulenhoff,
#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; Teemu Murtola, 
Szilard Pall, Sander Pronk, Roland Schulz,
#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
 Michael Shirts, Alfons Sijbers, Peter Tieleman,

#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
 Berk Hess, David van der Spoel, and Erik Lindahl.

#160;#160;#160;#160;#160;#160; Copyright (c) 1991-2000, University of 
Groningen, The Netherlands.
#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; Copyright 
(c) 2001-2010, The GROMACS development team at
#160;#160;#160;#160;#160;#160;#160; Uppsala University  The Royal 
Institute of Technology, Sweden.
#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; check out 
http://www.gromacs.org for more information.

#160;#160;#160;#160;#160;#160;#160;#160; This program is free software; 
you can redistribute it and/or
#160;#160;#160;#160;#160;#160;#160;#160;#160; modify it under the 
terms of the GNU General Public License
#160;#160;#160;#160;#160;#160;#160;#160; as published by the Free 
Software Foundation; either version 2
#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; of the 
License, or (at your option) any later version.

#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
 :-)#160; grompp#160; (-:

Option#160;#160;#160;#160; Filename#160; 
Type#160;#160;#160;#160;#160;#160;#160;#160; Description

#160; -f#160;#160;#160;#160;#160;#160; test.mdp#160; 
Input#160;#160;#160;#160;#160;#160;#160; grompp input file with MD 
parameters
#160;-po#160;#160;#160;#160;#160; mdout.mdp#160; 
Output#160;#160;#160;#160;#160;#160; grompp input file with MD parameters
#160; -c#160; ../3eq/eq.gro#160; 
Input#160;#160;#160;#160;#160;#160;#160; Structure file: gro g96 pdb tpr 
etc.
#160; -r#160;#160;#160;#160;#160;#160; conf.gro#160; Input, Opt.#160; 
Structure file: gro g96 pdb tpr etc.
#160;-rb#160;#160;#160;#160;#160;#160; conf.gro#160; Input, Opt.#160; 
Structure file: gro g96 pdb tpr etc.
#160; -n ../initial/index.ndx#160; Input, Opt!#160; Index file
#160; -p ../initial/insulin.top#160; 
Input#160;#160;#160;#160;#160;#160;#160; Topology file
#160;-pp#160; processed.top#160; Output, Opt. Topology file
#160; -o#160;#160;#160;#160;#160;#160; test.tpr#160; 
Output#160;#160;#160;#160;#160;#160; Run input file: tpr tpb tpa
#160; -t#160; ../3eq/eq.trr#160; Input, Opt!#160; Full precision 
trajectory: trr trj cpt
#160; -e#160;#160;#160;#160;#160;#160; ener.edr#160; Input, Opt.#160; 
Energy file

Option#160;#160;#160;#160;#160;#160; Type#160;#160; Value#160;#160; 
Description
--
-[no]h#160;#160;#160;#160;#160;#160; bool#160;#160; 
no#160;#160;#160;#160;#160; Print help info and quit
-[no]version bool#160;#160; no#160;#160;#160;#160;#160; Print version 
info and quit
-nice#160;#160;#160;#160;#160;#160;#160; int#160;#160;#160; 
0#160;#160;#160;#160;#160;#160; Set the nicelevel
-[no]v#160;#160;#160;#160;#160;#160; bool#160;#160; 
no#160;#160;#160;#160;#160; Be loud and noisy
-time#160;#160;#160;#160;#160;#160;#160; real#160;#160; 
-1#160;#160;#160;#160;#160; Take frame at or first after this time.
-[no]rmvsbds bool#160;#160; yes#160;#160;#160;#160; Remove constant 
bonded interactions with virtual
#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
 sites
-maxwarn#160;#160;#160;#160; int#160;#160;#160; 
0#160;#160;#160;#160;#160;#160; Number of allowed warnings during input
#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
 processing. Not for normal use and may generate
#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
 unstable systems
-[no]zero#160;#160;#160; bool#160;#160; no#160;#160;#160;#160;#160; 
Set parameters for bonded interactions without
#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;
 defaults to zero instead of

Re: [gmx-users] increasing cut-off and PME grid spacing

2011-08-20 Thread Justin A. Lemkul 



Hsin-Lin Chiang wrote:

Hi, Justin

Sorry for the unclear message.
My box vector in .gro file are 44.22834  44.22834  44.22834 and the 
number of atoms is 20171


You've set an unreasonably large box, as I expected.  The box should be set in 
nm, not Angstrom.  20171 atoms is a fairly small system, and in effect what 
you've created is a protein in a droplet of water, surrounded by vacuum.  90% of 
the work done by PME will be to calculate a grid of nothing.



The output of grompp is shown below,
I don't know if it is enough and I'm sorry I don't know how should I do 
after you reply.

Could you please give me more messages in detail?


The solution is to set a correct box, unless your objective is to simulate a 
droplet, in which case you have no choice but to take the performance loss 
inherent to using PME.


-Justin



Hsin-Lin
---
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
  Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
   Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,

   Berk Hess, David van der Spoel, and Erik Lindahl.

   Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University  The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

 This program is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License
 as published by the Free Software Foundation; either version 2
 of the License, or (at your option) any later version.

:-)  grompp  (-:

Option Filename  Type Description

  -f   test.mdp  Inputgrompp input file with MD parameters
 -po  mdout.mdp  Output   grompp input file with MD parameters
  -c  ../3eq/eq.gro  InputStructure file: gro g96 pdb tpr etc.
  -r   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
 -rb   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
  -n ../initial/index.ndx  Input, Opt!  Index file
  -p ../initial/insulin.top  InputTopology file
 -pp  processed.top  Output, Opt. Topology file
  -o   test.tpr  Output   Run input file: tpr tpb tpa
  -t  ../3eq/eq.trr  Input, Opt!  Full precision trajectory: trr trj cpt
  -e   ener.edr  Input, Opt.  Energy file

Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit
-[no]version bool   no  Print version info and quit
-niceint0   Set the nicelevel
-[no]v   bool   no  Be loud and noisy
-timereal   -1  Take frame at or first after this time.
-[no]rmvsbds bool   yes Remove constant bonded interactions with 
virtual

sites
-maxwarn int0   Number of allowed warnings during input
processing. Not for normal use and may generate
unstable systems
-[no]zerobool   no  Set parameters for bonded interactions without
defaults to zero instead of generating an error
-[no]renum   bool   yes Renumber atomtypes and minimize number of
atomtypes

Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#
Generated 279 of the 1225 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
turning H bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning H bonds into constraints...
Excluding 1 bonded neighbours molecule type 'NA'
turning H bonds into constraints...
Velocities were taken from a Maxwell distribution at 300 K
Number of degrees of freedom in T-Coupling group Protein is 1448.89
Number of degrees of freedom in T-Coupling group non-Protein is 39297.11
Reading Coordinates and Box size from old trajectory
Will read whole trajectory
Velocities generated: ignoring velocities in input trajectory
trn version: GMX_trn_file (single precision)
Last frame800 time  800.000
Using frame at t = 800 ps
Starting time for run is 0 ps
Largest charge group radii for Van der Waals: 0.248, 0.178 nm
Largest charge group radii for Coulomb:   0.248, 0.214 nm
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 224x224x224, spacing 0.197 0.197 0.197
Estimate for the relative computational load of the PME mesh part: 1.00

NOTE 1 [file test.mdp]:
  The optimal PME mesh load for parallel simulations is below 0.5
  and