[gmx-users] position restrain dynamics error

[Subramaniam Boopathi]

Dear Sir,
I am succesfully run molecules upto energy minimization, in case of
position restrain md step , i have following, could you help to overcome
the A charge group moved too far between two domain decomposition steps.

Step 1, time 0.002 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.021061, max 0.387149 (between atoms 360 and 363)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
360363   90.00.0960   0.1332  0.0960

Step 2, time 0.004 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.034712, max 0.636602 (between atoms 360 and 363)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
360363   90.10.1332   0.1571  0.0960

Back Off! I just backed up step2b_n7.pdb to ./#step2b_n7.pdb.1#

Back Off! I just backed up step2c_n7.pdb to ./#step2c_n7.pdb.1#
Wrote pdb files with previous and current coordinates

Step 3, time 0.006 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.023755, max 0.423951 (between atoms 360 and 363)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
360363   90.00.1571   0.1367  0.0960

Step 4, time 0.008 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.051081, max 0.931870 (between atoms 360 and 363)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
360363   90.30.1367   0.1855  0.0960

Back Off! I just backed up step4b_n7.pdb to ./#step4b_n7.pdb.1#

Back Off! I just backed up step4c_n7.pdb to ./#step4c_n7.pdb.1#
Wrote pdb files with previous and current coordinates

Step 5, time 0.01 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.020335, max 0.372790 (between atoms 360 and 363)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
360363   89.90.1855   0.1318  0.0960

Step 6, time 0.012 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.056021, max 1.029913 (between atoms 360 and 363)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
360363   90.20.1318   0.1949  0.0960

Back Off! I just backed up step6b_n7.pdb to ./#step6b_n7.pdb.2#

Back Off! I just backed up step6c_n7.pdb to ./#step6c_n7.pdb.2#
Wrote pdb files with previous and current coordinates

Step 7, time 0.014 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.024586, max 0.451876 (between atoms 360 and 363)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
360363   90.00.1949   0.1394  0.0960

with regards
S. Boopathi
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[gmx-users] PCA_RMS fluctuation per residue?

[라지브간디]

Message: 5 
Date: Wed, 8 May 2013 08:25:33 +0200 
From: Tsjerk Wassenaar  
Subject: Re: [gmx-users] PCA_RMS fluctuation per residue? 
To: Discussion list for GROMACS users  
Message-ID: 
 
Content-Type: text/plain; charset=UTF-8 

Thank you for the reply Tsjerk.




Could you tell me how i can visualize the motion s of eigenvectors ?  I read 
from somewhere, In order to reveal the 3d motions via VMD/chimera have to add 
the msd value in filtered pdb file of eigenvector? If that so, how it can be 
done?




Hi Rajiv, 

Square the values, sum them per residue and take the square root. 

Cheers, 

Tsjerk 

On May 8, 2013 7:24 AM, "���"  wrote: 

Dear gmx users, 


I've done covariance matrix for backbone of protein using g_covar command. 


Also, can able to plot all projections through g_anaeig. 


However, I could only able to do -rmsf: plot the RMS fluctuation per atom 
of eigenvectors BUT i wants to do them per residue? How can i achieve this? 


In manual it shows -filt: command filter the trajectory to show only the 
motion along eigenvectors. How i do visualize this kind of motions? 

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Re: [gmx-users] Usage of g_spatial

[Venkat Reddy]

Sir

Yes, trjconv works without tpr. Thanks for that.

I want to see the distribution of anion around cation. Is it not possible
to see an averaged spatial distribution of all anions around all cations?
Do I need to make a selection of a single cation molecule?

I did the selection of a single cation molecule which is approximately at
the center of the box and did the following

step 1: trjconv -s 1md.pdb -f 11md_gro.pdb -o 11md_gro_mod.pdb -center -ur
compact -pbc none
when it asked for group for centering and output, I selected the whole
system for both.

step 2: trjconv -s 1md.pdb -f 11md_gro_mod.pdb -o 11md_gro_mod1.pdb -fit
rot+trans
when it asked for group for least square once again I selected the whole
system

I selected the whole system as a previous discussion
http://lists.gromacs.org/pipermail/gmx-users/2010-May/050879.html

suggested the same because of an error that was happening in step 2.

*Fatal error: Index[2385] 2410 is larger than the number of atoms in**
the trajectory file (2409).
*
Since I was getting the same error if I made any form of selections in
the first two steps, I output the whole system.

step 3: g_spatial. and used ANI as group to generate SDF and a single
cation residue as the group to output coords

When I loaded the resultant cube in vmd I could see the whole
distribution.

Where am I going wrong?



On Tue, May 7, 2013 at 6:23 PM, Christopher Neale <
chris.ne...@mail.utoronto.ca> wrote:

> Try this:
>
> trjconv -s my.pdb -f my.pdb -o mymod.pdb
> g_spatial -s mymod.pdb -f mymod.pdb
>
> For the pre-processing, there must also be AMBER tools that will do this
> for you if for some reason the above does not work for you (e.g. Option
> -pbc mol requires a .tpr file for the -s option)
>
> Chris.
>
> -- original message --
>
> I am analyzing trajectories of an ionic liquid system generated using AMBER
> MD package. The force field parameters are typical of this IL system and
> not from the existing libraries. Hence, it is difficult for me to generate
> a tpr file. I understand that running the g_spatial command needs
> pre-processing of the coordinates (Steps 1 and 2 in g_spatial help) but I
> need tpr file for that. So there is  no way of doing g_spatial without a
> tpr file is it? Then how do I generate tpr file for my system?
>
> Thanks for all the help
> --
> --
> gmx-users mailing listgmx-users@gromacs.org
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>



-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036


On Tue, May 7, 2013 at 6:23 PM, Christopher Neale <
chris.ne...@mail.utoronto.ca> wrote:

> Try this:
>
> trjconv -s my.pdb -f my.pdb -o mymod.pdb
> g_spatial -s mymod.pdb -f mymod.pdb
>
> For the pre-processing, there must also be AMBER tools that will do this
> for you if for some reason the above does not work for you (e.g. Option
> -pbc mol requires a .tpr file for the -s option)
>
> Chris.
>
> -- original message --
>
> I am analyzing trajectories of an ionic liquid system generated using AMBER
> MD package. The force field parameters are typical of this IL system and
> not from the existing libraries. Hence, it is difficult for me to generate
> a tpr file. I understand that running the g_spatial command needs
> pre-processing of the coordinates (Steps 1 and 2 in g_spatial help) but I
> need tpr file for that. So there is  no way of doing g_spatial without a
> tpr file is it? Then how do I generate tpr file for my system?
>
> Thanks for all the help
> --
> --
> gmx-users mailing listgmx-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!
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> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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[gmx-users] error in running distances.pl

[Arunima Shilpi]

Hello Sir

While running command for perl distances.pl.. system gets hanged...while
processing  particular group file...

I will be thankful to you if you can guide me in debugging the error
-- 

Thanking You with Regards.

Arunima Shilpi

Ph. D Research Scholar(Cancer & Epigenetics)
Department of Life Science
National Institute of Technology
Rourkela
Odisha
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Re: [gmx-users] error in running distances.pl

[Justin Lemkul]

On 5/8/13 8:16 AM, Arunima Shilpi wrote:

Hello Sir

While running command for perl distances.pl.. system gets hanged...while
processing  particular group file...

I will be thankful to you if you can guide me in debugging the error



If you created groups.txt in accordance with what the tutorial says and your 
index file contains the necessary groups (again, explained in the tutorial), 
there should be no problem.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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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Re: [gmx-users] position restrain dynamics error

[Justin Lemkul]

On 5/8/13 3:07 AM, Subramaniam Boopathi wrote:

Dear Sir,
 I am succesfully run molecules upto energy minimization, in case of
position restrain md step , i have following, could you help to overcome
the A charge group moved too far between two domain decomposition steps.

Step 1, time 0.002 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.021061, max 0.387149 (between atoms 360 and 363)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
 360363   90.00.0960   0.1332  0.0960

Step 2, time 0.004 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.034712, max 0.636602 (between atoms 360 and 363)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
 360363   90.10.1332   0.1571  0.0960

Back Off! I just backed up step2b_n7.pdb to ./#step2b_n7.pdb.1#

Back Off! I just backed up step2c_n7.pdb to ./#step2c_n7.pdb.1#
Wrote pdb files with previous and current coordinates

Step 3, time 0.006 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.023755, max 0.423951 (between atoms 360 and 363)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
 360363   90.00.1571   0.1367  0.0960

Step 4, time 0.008 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.051081, max 0.931870 (between atoms 360 and 363)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
 360363   90.30.1367   0.1855  0.0960

Back Off! I just backed up step4b_n7.pdb to ./#step4b_n7.pdb.1#

Back Off! I just backed up step4c_n7.pdb to ./#step4c_n7.pdb.1#
Wrote pdb files with previous and current coordinates

Step 5, time 0.01 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.020335, max 0.372790 (between atoms 360 and 363)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
 360363   89.90.1855   0.1318  0.0960

Step 6, time 0.012 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.056021, max 1.029913 (between atoms 360 and 363)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
 360363   90.20.1318   0.1949  0.0960

Back Off! I just backed up step6b_n7.pdb to ./#step6b_n7.pdb.2#

Back Off! I just backed up step6c_n7.pdb to ./#step6c_n7.pdb.2#
Wrote pdb files with previous and current coordinates

Step 7, time 0.014 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.024586, max 0.451876 (between atoms 360 and 363)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
 360363   90.00.1949   0.1394  0.0960



http://www.gromacs.org/Documentation/Terminology/Blowing_Up

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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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Re: [gmx-users] unstable system

[Justin Lemkul]

On 5/8/13 2:35 AM, Shima Arasteh wrote:

OK.

1. Exact commands given in the preparation protocol (EM and equilibration)

EM:
# grompp -f minim.mdp -c input.gro -p topol.top -o minim.tpr
#mdrun -deffnm minim

NVT:
#grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr
#mdrun -deffnm nvt -v

NPT:
# grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -n index.ndx -o npt.tpr
# mdrun_mpi -deffnm npt


*** Next removed some disturbing water molecules, so edited topol file and made 
a new index file index_mod_2.ndx:
Ran a new EM:
# grompp -f npt.mdp -c npt_mod.gro -p topol.top -o npt_minim.tpr
# mdrun -deffnm npt_minim


Ran a new NPT:
# grompp -f npt.mdp -c npt_minim.gro -p topol.top -n index_mod_2.ndx -o npt.tpr
# mdrun_mpi -deffnm npt

I repeated the NPT the same as above in 3 steps:
a) restraints on lipid phosphorous and protein for 1 ns

b) restraints on protein for 1ns

c) restraint on protein with less force for 2 ns



All 3 of these steps complete successfully?



MD:
# grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index_mod_2.ndx -o 
md_0_1.tpr
# mdrun -deffnm npt



There are a few discrepancies in the commands you have shown here, in particular 
naming differences between input and output file names.  I ask for exact 
commands (not what you think you remember) for a very important reason - the 
diagnostic information you have provided (from the .log file) seems to indicate 
that the previous equilibrated state was not passed along to the MD step, so I 
suspect you've left out a checkpoint file somewhere or you have regenerated 
velocities by accident.


As a tip, write all of your commands in a shell script and execute the script. 
Then, if something goes wrong and someone asks for exact commands, just copy and 
paste.  I still can't tell if this is actually what you did.




3 particles communicated to PME node 2 are more than 2/3 times the cut -
off out of the domain decomposition cell of their charge group in
dimension y.
This usually means that your system is not well equilibrated.


2. The .mdp files being used for all steps, most importantly NPT and MD

npt.mdp:

;NPT equlibration Dimer-POPC-Water - CHARMM36
define= -DPOSRES
integrator  = md; leap-frog integrator
nsteps  =100 ; 1 * 100 = 1000 ps
dt  = 0.001 ; 1 fs
; Output control
nstxout = 2000  ; save coordinates every 0.4 ps
nstvout = 2000   ; save velocities every 0.2 ps
nstenergy   = 1000   ; save energies every 0.2 ps
nstlog  = 1000   ; update log file every 0.2 ps

continuation= yes; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = h-bonds ; all bonds (even heavy atom-H bonds) constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist   = 1.2   ; short-range neighborlist cutoff (in nm)
rlistlong   = 1.4
rcoulomb= 1.2   ; short-range electrostatic cutoff (in nm)
rvdw= 1.2   ; short-range van der Waals cutoff (in nm)
vdwtype = switch
rvdw_switch = 1.0
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range 
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = Nose-Hoover ; modified Berendsen thermostat
tc-grps = Protein_POPCWater_and_ions; two coupling groups - 
more accurate
tau_t   = 0.5   0.5   ; time constant, in ps
ref_t   = 310   310 ; reference temperature, one for each group, in 
K
pcoupl  = Berendsen; no pressure coupling in NVT
pcoupltype  = semiisotropic
tau_p   = 4
ref_p   = 1.01325 1.01325
compressibility = 4.5e-5 4.5e-5

; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= no; account for cut-off vdW scheme
; Velocity generation
gen_vel = no   ; assign velocities from Maxwell distribution
;gen_temp   = 310   ; temperature for Maxwell distribution
;gen_seed   = -1; generate a random seed
nstcomm = 1
comm_mode   = Linear
comm_grps   = Protein_POPC Water_and_ions
refcoord_scaling = com


md.mdp:

title= Production run forGLC-Water-POPC system
define= -DPOSRES
; Parameters describing the details of the NVT simulation protocol
integrator= md
dt= 0.001
nsteps= 250; Number of steps to run (0.002 * 250 = 5 ns)

; Parameters controlling output writing
nstxout= 1000; Write coordinates to output .trr file every 10 ps
nstvout= 2000; Write velo

[gmx-users] Problem with DSSP

[Sainitin Donakonda]

Hello,

I am trying to secondary structure analysis using DSSP in gromacs so i
followed this procedure

First I downloaded dssp

wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64  -O
~/dssp

this gave dssp executable file in my home directory

I checked ./dssp ...it works

Then i set environment variable as follows

export DSSP=/myhomedir/dssp/dssp

then i executed following command in gromacs

do_dssp -f protein.xtc -s protein.tpr -sc scount.xvg -o ss.xpm -dt 10

But this gives following error

*Program do_dssp, VERSION 4.5.4
Source code file:
/home/toor/gromacs/gromacs-4.5.4/src/tools/do_dssp.c, line: 516

Fatal error:
DSSP executable (/home/dssp) does not exist (use setenv DSSP)*

*
*

*Can any body explain where it went wrong...*

*I have gone through gromacs list but unfortunately couldnot manage to
solve this simple issue*

*
*

*Thanks,*

*Nitin*
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Re: [gmx-users] Problem with DSSP

[Erik Marklund]

/home/dssp seems like a strange path. Are you sure you set DSSP correctly?

Erik
 
On 8 May 2013, at 15:19, Sainitin Donakonda  wrote:

> Hello,
> 
> I am trying to secondary structure analysis using DSSP in gromacs so i
> followed this procedure
> 
> First I downloaded dssp
> 
> wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64  -O
> ~/dssp
> 
> this gave dssp executable file in my home directory
> 
> I checked ./dssp ...it works
> 
> Then i set environment variable as follows
> 
> export DSSP=/myhomedir/dssp/dssp
> 
> then i executed following command in gromacs
> 
> do_dssp -f protein.xtc -s protein.tpr -sc scount.xvg -o ss.xpm -dt 10
> 
> But this gives following error
> 
> *Program do_dssp, VERSION 4.5.4
> Source code file:
> /home/toor/gromacs/gromacs-4.5.4/src/tools/do_dssp.c, line: 516
> 
> Fatal error:
> DSSP executable (/home/dssp) does not exist (use setenv DSSP)*
> 
> *
> *
> 
> *Can any body explain where it went wrong...*
> 
> *I have gone through gromacs list but unfortunately couldnot manage to
> solve this simple issue*
> 
> *
> *
> 
> *Thanks,*
> 
> *Nitin*
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] Problem with DSSP

[Justin Lemkul]

On 5/8/13 9:19 AM, Sainitin Donakonda wrote:

Hello,

I am trying to secondary structure analysis using DSSP in gromacs so i
followed this procedure

First I downloaded dssp

wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64  -O
~/dssp

this gave dssp executable file in my home directory

I checked ./dssp ...it works

Then i set environment variable as follows

export DSSP=/myhomedir/dssp/dssp

then i executed following command in gromacs

do_dssp -f protein.xtc -s protein.tpr -sc scount.xvg -o ss.xpm -dt 10

But this gives following error

*Program do_dssp, VERSION 4.5.4
Source code file:
/home/toor/gromacs/gromacs-4.5.4/src/tools/do_dssp.c, line: 516

Fatal error:
DSSP executable (/home/dssp) does not exist (use setenv DSSP)*

*
*

*Can any body explain where it went wrong...*



Apparently you set the environment variable wrong.  When reporting problems, 
please be exact.  You have an export statement above that does not match what 
do_dssp actually finds.  We don't know where your files are or how you've 
organized things.  The DSSP environment variable needs to point to the dssp 
executable itself, not the directory containing it.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] fw: hey

[Wholly Peach]

http://www.verbatim-vnet.com/wvazkeegoblnf.php 













 Breakthrough Diet Exposed: Celebrity Doctor Uncovers The "Holy Grail of Weight 
Loss" 












 





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[gmx-users] g_select question

[Albert]

Dear:

 I am trying to run g_select with command:

g_select -f md.xtc -s md.pdb -os water.xvg -sf selection.dat

in the selection.dat I defined the following:


watero= name 0 and resname T3P;
close = water0 and within 0.6 of resid 50;
close;

my residue 50 is in the deep pocket of protein and there is only max. 12 
water near 6A. However, I found that in almost all my trajectories, 
there are at least 16 water from the g_select output. I am just 
wondering, is there anything wrong of my defenition in selection.dat?


thank you very much

best
Albert
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Re: [gmx-users] Langevin thermostat implementation in GROMACS vs AMBER

[Julian Garrec]

No suggestion ?? :)

In my post I forgot to say that my system contains explicit water.

I'm still very curious about the difference in implementation in AMBER 
and GROMACS. And I still don't really understand the meanning of tau-t 
in LD and how  it is related to other (well defined) quantities such as 
the friction coeficient in equation 3.114 of the manual (v4.6.1).


Please help,

Sincerely,

Julian


Le 04/05/13 13:42, Julian Garrec a écrit :

Dear all,

I am trying to use stochastic dynamics in GROMACS to reproduce some 
previous results that I got with the AMBER software using the Langevin 
thermostat.


In AMBER, one typically sets what they call the "collision frequency" 
(noted gamma_ln in the AMBER manual). I typically set gamma_ln to 2 
collisions per ps (significantly smaller than the internal friction of 
water, since I use Langevin dynamics as a thermostat).


1) In the mdp options manual, it is recommended to use {integrator=sd 
; bd-fric=0 ; tau-t=2}. My understanding is that bd-fric corresponds 
to 'm_i*gamma_i' in equation 3.114 of the theoretical part of the 
manual (version 4.6.1). Am I right ?


2) Then, is {integrator=sd ; bd-fric=0 ; tau-t=2} equivalent to 
{integrator=sd ; bd-fric=0.5} ? (In the theoretical part of the 
manual, it is said that gamma_i should be set to 0.5 to follow the 
same spirit).


3) Is 'bd-fric' of GROMACS equivalent to 'gamm_ln' of AMBER ?

Thanks for your help,

Julian




--
Julian Garrec, research associate

Web: https://sites.google.com/site/juliangarrec/

Équipe : Chimie et Biochimie Théoriques
Unité Mixte de Recherches CNRS UHP 7565
Université de Lorraine, Nancy I BP 239,
54506 Vandoeuvre-lès-Nancy, cedex France

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[gmx-users] Cut off setting

[Wende Tian]

Hi everyone,


I want to calculate the LJ potential with different Cut-off for simulation
in a reduced unit (LJ unit).


For example, the cut-off for  LJ potential of A-A, A-B, and B-B is 1.12246
(repulsive), 1.12246, and 2.5 （attractive, respectively;


However, it seems that the Cut-off only can be set once. How to deal with
the problem except tables?  Thanks in advance!




-- 
Best Wishes From Suzhou, China

Wade
--
Wen-de Tian (田文得), Ph. D
Email : tianwe...@suda.edu.cn
Website : http://scm.suda.edu.cn/pweb/csmpg

Center for Soft Condensed Matter Physics and Interdisciplinary Research,
Soochow University,
Suzhou 215006,
China

通讯地址：苏州大学软凝聚态物理及交叉研究中心,苏州市十梓街1号，215006
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[gmx-users] mdp-settings for charmm36 and lipid apl values

[Gmx QA]

Hi gmx-users,

I've been experimenting with simulations of mixed bilayers (512 lipids in
total, 70% POPC, 30% POPE) using the charmm36 parameter set in gromacs, and
have a couple of questions. I know this has been discussed before, but I'd
appreciate some input nonetheless :-)

The relevant sections of my mdp-file are pasted below:

; Start time and timestep in ps
tinit= 0
dt   = 0.001
nsteps   = 1

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist  = 5
; ns algorithm (simple or grid)
ns_type  = grid
; Periodic boundary conditions: xyz, no, xy
pbc  = xyz
periodic_molecules   = no
; nblist cut-off
rlist= 1.2
; long-range cut-off for switched potentials
rlistlong= 1.4

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = PME
rcoulomb-switch  = 0
rcoulomb = 1.2
; Relative dielectric constant for the medium and the reaction field
epsilon_r= 1
epsilon_rf   = 1
; Method for doing Van der Waals
vdw-type = switch
; cut-off lengths
rvdw-switch  = 0.8
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = No

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
tcoupl   = V-rescale
nsttcouple   = -1
nh-chain-length  = 10
; Groups to couple separately
tc-grps  = System
; Time constant (ps) and reference temperature (K)
tau_t= 0.1
ref_t= 300
; Pressure coupling
pcoupl   = Parrinello-Rahman
pcoupltype   = semiisotropic
nstpcouple   = -1

This is as far as I can tell from earlier discussions on the list, and also
from reading the Piggott et al. paper in JCTC, the correct settings for
charmm36.

After a simulation of ~50 ns, I use GridMatMD to calculate the area per
headgroup of POPC and POPE, respectively, and get what I think are not 100%
acceptable results (but maybe they are)

For POPC, I get 59,7 A^2, and for POPE, I get 63,1 A^2.

The value for POPE would have been fine I suppose if it hadn't been for the
fact that the APL for POPC is smaller. Should it not be larger than POPE?

I notice in the Piggott-paper that they in the supplement for some
simulations of POPC also get APL's of around 59-60 (without POPE of
course), and that the results depend to some extent also on the usage of
TIP3P vs TIP3SP water models. I have been using "normal" TIP3P here.

Could anyone comment on (a) my mdp-file settings, and (b) the resulting
APL, and tell me if I should be worried about anything?

THANKS
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Re: [gmx-users] unstable system

[Shima Arasteh]

Yes, all steps were completed successfully.
About your tips, OK sir.

I' m going to go through the minimization and NVT and NPT again. Lets get my 
result, then will post the exact commands.

Thanks for your suggestions.


 
Sincerely,
Shima


- Original Message -
From: Justin Lemkul 
To: Shima Arasteh ; Discussion list for GROMACS 
users 
Cc: 
Sent: Wednesday, May 8, 2013 5:07 PM
Subject: Re: [gmx-users] unstable system



On 5/8/13 2:35 AM, Shima Arasteh wrote:
> OK.
>
> 1. Exact commands given in the preparation protocol (EM and equilibration)
>
> EM:
> # grompp -f minim.mdp -c input.gro -p topol.top -o minim.tpr
> #mdrun -deffnm minim
>
> NVT:
> #grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr
> #mdrun -deffnm nvt -v
>
> NPT:
> # grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -n index.ndx -o npt.tpr
> # mdrun_mpi -deffnm npt
>
>
> *** Next removed some disturbing water molecules, so edited topol file and 
> made a new index file index_mod_2.ndx:
> Ran a new EM:
> # grompp -f npt.mdp -c npt_mod.gro -p topol.top -o npt_minim.tpr
> # mdrun -deffnm npt_minim
>
>
> Ran a new NPT:
> # grompp -f npt.mdp -c npt_minim.gro -p topol.top -n index_mod_2.ndx -o 
> npt.tpr
> # mdrun_mpi -deffnm npt
>
> I repeated the NPT the same as above in 3 steps:
> a) restraints on lipid phosphorous and protein for 1 ns
>
> b) restraints on protein for 1ns
>
> c) restraint on protein with less force for 2 ns
>

All 3 of these steps complete successfully?

>
> MD:
> # grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index_mod_2.ndx -o 
> md_0_1.tpr
> # mdrun -deffnm npt
>

There are a few discrepancies in the commands you have shown here, in 
particular 
naming differences between input and output file names.  I ask for exact 
commands (not what you think you remember) for a very important reason - the 
diagnostic information you have provided (from the .log file) seems to indicate 
that the previous equilibrated state was not passed along to the MD step, so I 
suspect you've left out a checkpoint file somewhere or you have regenerated 
velocities by accident.

As a tip, write all of your commands in a shell script and execute the script. 
Then, if something goes wrong and someone asks for exact commands, just copy 
and 
paste.  I still can't tell if this is actually what you did.

>
> 3 particles communicated to PME node 2 are more than 2/3 times the cut -
> off out of the domain decomposition cell of their charge group in
> dimension y.
> This usually means that your system is not well equilibrated.
>
>
> 2. The .mdp files being used for all steps, most importantly NPT and MD
>
> npt.mdp:
>
> ;NPT equlibration Dimer-POPC-Water - CHARMM36
> define        = -DPOSRES
> integrator      = md            ; leap-frog integrator
> nsteps          =100         ; 1 * 100 = 1000 ps
> dt              = 0.001         ; 1 fs
> ; Output control
> nstxout         = 2000          ; save coordinates every 0.4 ps
> nstvout         = 2000           ; save velocities every 0.2 ps
> nstenergy       = 1000           ; save energies every 0.2 ps
> nstlog          = 1000           ; update log file every 0.2 ps
>
> continuation    = yes            ; first dynamics run
> constraint_algorithm = lincs    ; holonomic constraints
> constraints     = h-bonds     ; all bonds (even heavy atom-H bonds) 
> constrained
> lincs_iter      = 1             ; accuracy of LINCS
> lincs_order     = 4             ; also related to accuracy
> ; Neighborsearching
> ns_type         = grid          ; search neighboring grid cells
> nstlist         = 5             ; 10 fs
> rlist           = 1.2           ; short-range neighborlist cutoff (in nm)
> rlistlong       = 1.4
> rcoulomb        = 1.2           ; short-range electrostatic cutoff (in nm)
> rvdw            = 1.2           ; short-range van der Waals cutoff (in nm)
> vdwtype         = switch
> rvdw_switch     = 1.0
> ; Electrostatics
> coulombtype     = PME           ; Particle Mesh Ewald for long-range 
> electrostatics
> pme_order       = 4             ; cubic interpolation
> fourierspacing  = 0.16          ; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl          = Nose-Hoover     ; modified Berendsen thermostat
> tc-grps         = Protein_POPC    Water_and_ions    ; two coupling groups - 
> more accurate
> tau_t           = 0.5   0.5       ; time constant, in ps
> ref_t           = 310   310     ; reference temperature, one for each group, 
> in K
> pcoupl          = Berendsen            ; no pressure coupling in NVT
> pcoupltype      = semiisotropic
> tau_p           = 4
> ref_p           = 1.01325 1.01325
> compressibility = 4.5e-5 4.5e-5
>
> ; Periodic boundary conditions
> pbc             = xyz           ; 3-D PBC
> ; Dispersion correction
> DispCorr        = no    ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel         = no           ; assign velocities from Maxwell distribution
> ;gen_temp       = 310           ; temperature for Maxwel

Re: [gmx-users] g_select question

[Teemu Murtola]

Hi,

On Wed, May 8, 2013 at 4:44 PM, Albert  wrote:

> I am trying to run g_select with command:
>
> g_select -f md.xtc -s md.pdb -os water.xvg -sf selection.dat
>
> in the selection.dat I defined the following:
>
> watero= name 0 and resname T3P;
> close = water0 and within 0.6 of resid 50;
> close;
>
> my residue 50 is in the deep pocket of protein and there is only max. 12
> water near 6A. However, I found that in almost all my trajectories, there
> are at least 16 water from the g_select output. I am just wondering, is
> there anything wrong of my defenition in selection.dat?
>

There's nothing obvious wrong with the selections (if you don't count
mismatches between the letter O and the number 0, which should give you
errors if you really had those in your input). You can try to diagnose the
issue with the -oi and/or -on flags for g_select to see what exactly gets
selected. You should also ensure that "resid 50" selects the residue you
expect and nothing else.

If you think that something is getting selected incorrectly, please provide
additional information like your Gromacs versions and what exactly is
selected and why it shouldn't.

Teemu
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RE: [gmx-users] Viscosity calculation using cos_acceleration

[Berk Hess]

Hi,

I "fixed" an issue with the 1/visc output in 4.5.4, but incorretly.
I filed a bug report and a fix, you can easily correct your numbers:
http://redmine.gromacs.org/issues/1244
https://gerrit.gromacs.org/#/c/2370/

Thanks for reporting this.

Cheers,

Berk

> Date: Thu, 11 Apr 2013 16:55:37 +0900
> From: jamesresearch...@gmail.com
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Viscosity calculation using cos_acceleration
> 
> Dear Gromacs users,
> 
> This question seems to come up periodically in the mailing list, but none
> of the previous answers seem helpful in my case.
> 
> I'm trying to reproduce the viscosity calculation of SPC water by Berk Hess
> (JCP 116, 2002) using cos_acceleration in Gromacs. The answer I get is 2
> orders of magnitude out.
> 
> My topology file and parameter file is appended at the bottom of this email.
> 
> I run g_energy and get
> 
> Energy  Average   Err.Est.   RMSD  Tot-Drift
> ---
> 1/Viscosity 23.4689   0.132.39126  -0.255371  (m
> s/kg)
> 
> which gives a viscosity of 0.04 kg/(m s), or 40 mPa.s
> 
> The value quoted in the paper is about 0.4 mPa.s which is around the
> correct value for water, give or take a bit.
> 
> So my question is, where is my missing factor of 100?
> 
> Any advice is much appreciated.
> 
> Thank you.
> 
> James
> 
> --
> Topology file:
> #include "ffgmx.itp"
> #include "spc.itp"
> 
> [ system ]
> Pure Water
> 
> [ molecules ]
> SOL 3456
> 
> --
> Parameter file for system (3456 SPC water molecules, 3.75x3.75x7.5 nm3 box):
> 
> ;Generic mdp file for SPC water equilibration
> ;Gromacs 4.3.x
> ;
> ;T = 300 K
> ;
> ;NVT 1.2 ns
> ;
> 
> define   =  ; define here posres etc., e.g. -DPOSRES
> 
> integrator  = md
> tinit   = 0
> dt  = 0.001
> nsteps  = 120
> 
> ; Bond constraints
> continuation = no ; switch to 'yes' if need to read in velocities etc.
> constraints =  none; constrain all bond lengths
> constraint_algorithm=  lincs   ; default
> lincs_order =  4   ; default
> 
> nstxout = 1000
> nstvout = 1000
> nstfout = 0
> nstlog  = 1000
> nstenergy   = 1000
> ; Output frequency and precision for xtc file
> nstxtcout   = 1000
> xtc-precision   = 1000
> ; This selects the subset of atoms for the xtc file. You can
> ; select multiple groups. By default all atoms will be written.
> xtc-grps=
> ; Selection of energy groups
> energygrps  = System
> 
> ; Neighbor list
> ns_type  =  grid; neighlist type
> nstlist  =  5   ; Freq. to update neighbour list
> rlist=  0.9 ; nm (cutoff for short-range NL)
> pbc = xyz
> periodic_molecules   =  no
> 
> ; Non-equilibrium MD
> ;acc_grps = SYSTEM
> cos_acceleration = 0.025 ; PPM option for viscosity calculation (nm/ps²)
> coulombtype  = PME
> rcoulomb = 0.9
> optimize_fft = yes ; affects only PME calculations
> ; if you use PME, set also rcoulomb = rlist
> ; van der Waals interactions
> vdwtype  =  Cut-off; Van der Waals interactions
> rvdw =  0.9; nm (LJ cut-off)
> DispCorr = EnerPres ; long-range dispersion correction to energy and
> pressure
> 
> Tcoupl  = berendsen
> tc-grps = System
> tau_t   = 2.5
> ref_t   = 300.0
> 
> ;Pressure coupling
> Pcoupl = no
> gen_vel = no
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at 
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> www interface or send it to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] mdp-settings for charmm36 and lipid apl values

[Justin Lemkul]

On 5/8/13 11:09 AM, Gmx QA wrote:

Hi gmx-users,

I've been experimenting with simulations of mixed bilayers (512 lipids in
total, 70% POPC, 30% POPE) using the charmm36 parameter set in gromacs, and
have a couple of questions. I know this has been discussed before, but I'd
appreciate some input nonetheless :-)

The relevant sections of my mdp-file are pasted below:

; Start time and timestep in ps
tinit= 0
dt   = 0.001
nsteps   = 1

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist  = 5
; ns algorithm (simple or grid)
ns_type  = grid
; Periodic boundary conditions: xyz, no, xy
pbc  = xyz
periodic_molecules   = no
; nblist cut-off
rlist= 1.2
; long-range cut-off for switched potentials
rlistlong= 1.4

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = PME
rcoulomb-switch  = 0
rcoulomb = 1.2
; Relative dielectric constant for the medium and the reaction field
epsilon_r= 1
epsilon_rf   = 1
; Method for doing Van der Waals
vdw-type = switch
; cut-off lengths
rvdw-switch  = 0.8
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = No

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
tcoupl   = V-rescale
nsttcouple   = -1
nh-chain-length  = 10
; Groups to couple separately
tc-grps  = System
; Time constant (ps) and reference temperature (K)
tau_t= 0.1
ref_t= 300
; Pressure coupling
pcoupl   = Parrinello-Rahman
pcoupltype   = semiisotropic
nstpcouple   = -1

This is as far as I can tell from earlier discussions on the list, and also
from reading the Piggott et al. paper in JCTC, the correct settings for
charmm36.

After a simulation of ~50 ns, I use GridMatMD to calculate the area per
headgroup of POPC and POPE, respectively, and get what I think are not 100%
acceptable results (but maybe they are)

For POPC, I get 59,7 A^2, and for POPE, I get 63,1 A^2.

The value for POPE would have been fine I suppose if it hadn't been for the
fact that the APL for POPC is smaller. Should it not be larger than POPE?

I notice in the Piggott-paper that they in the supplement for some
simulations of POPC also get APL's of around 59-60 (without POPE of
course), and that the results depend to some extent also on the usage of
TIP3P vs TIP3SP water models. I have been using "normal" TIP3P here.

Could anyone comment on (a) my mdp-file settings, and (b) the resulting
APL, and tell me if I should be worried about anything?



The .mdp settings are fine as far as I can tell.  If you're concerned about 
accuracy, you should be analyzing a known system and trying to reproduce it. 
There is no reason in my mind why a binary lipid system should produce the 
behavior of a pure lipid system.  Lipids affect each other (just like all 
molecules do).  Headgroup interactions and acyl chain packing get more complex 
with increasing numbers of different lipids.


-Justin

--


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Research Scientist
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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Re: [gmx-users] mdp-settings for charmm36 and lipid apl values

[Gmx QA]

Thanks Justin, those are good points.

A quick follow up, would you (or someone else) consider the APL-values I
have for my mixed bilayer system to be good, just ok-ish or plain wrong?

THANKS



2013/5/8 Justin Lemkul 

>
>
> On 5/8/13 11:09 AM, Gmx QA wrote:
>
>> Hi gmx-users,
>>
>> I've been experimenting with simulations of mixed bilayers (512 lipids in
>> total, 70% POPC, 30% POPE) using the charmm36 parameter set in gromacs,
>> and
>> have a couple of questions. I know this has been discussed before, but I'd
>> appreciate some input nonetheless :-)
>>
>> The relevant sections of my mdp-file are pasted below:
>>
>> ; Start time and timestep in ps
>> tinit= 0
>> dt   = 0.001
>> nsteps   = 1
>>
>> ; NEIGHBORSEARCHING PARAMETERS
>> ; nblist update frequency
>> nstlist  = 5
>> ; ns algorithm (simple or grid)
>> ns_type  = grid
>> ; Periodic boundary conditions: xyz, no, xy
>> pbc  = xyz
>> periodic_molecules   = no
>> ; nblist cut-off
>> rlist= 1.2
>> ; long-range cut-off for switched potentials
>> rlistlong= 1.4
>>
>> ; OPTIONS FOR ELECTROSTATICS AND VDW
>> ; Method for doing electrostatics
>> coulombtype  = PME
>> rcoulomb-switch  = 0
>> rcoulomb = 1.2
>> ; Relative dielectric constant for the medium and the reaction field
>> epsilon_r= 1
>> epsilon_rf   = 1
>> ; Method for doing Van der Waals
>> vdw-type = switch
>> ; cut-off lengths
>> rvdw-switch  = 0.8
>> rvdw = 1.2
>> ; Apply long range dispersion corrections for Energy and Pressure
>> DispCorr = No
>>
>> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
>> ; Temperature coupling
>> tcoupl   = V-rescale
>> nsttcouple   = -1
>> nh-chain-length  = 10
>> ; Groups to couple separately
>> tc-grps  = System
>> ; Time constant (ps) and reference temperature (K)
>> tau_t= 0.1
>> ref_t= 300
>> ; Pressure coupling
>> pcoupl   = Parrinello-Rahman
>> pcoupltype   = semiisotropic
>> nstpcouple   = -1
>>
>> This is as far as I can tell from earlier discussions on the list, and
>> also
>> from reading the Piggott et al. paper in JCTC, the correct settings for
>> charmm36.
>>
>> After a simulation of ~50 ns, I use GridMatMD to calculate the area per
>> headgroup of POPC and POPE, respectively, and get what I think are not
>> 100%
>> acceptable results (but maybe they are)
>>
>> For POPC, I get 59,7 A^2, and for POPE, I get 63,1 A^2.
>>
>> The value for POPE would have been fine I suppose if it hadn't been for
>> the
>> fact that the APL for POPC is smaller. Should it not be larger than POPE?
>>
>> I notice in the Piggott-paper that they in the supplement for some
>> simulations of POPC also get APL's of around 59-60 (without POPE of
>> course), and that the results depend to some extent also on the usage of
>> TIP3P vs TIP3SP water models. I have been using "normal" TIP3P here.
>>
>> Could anyone comment on (a) my mdp-file settings, and (b) the resulting
>> APL, and tell me if I should be worried about anything?
>>
>>
> The .mdp settings are fine as far as I can tell.  If you're concerned
> about accuracy, you should be analyzing a known system and trying to
> reproduce it. There is no reason in my mind why a binary lipid system
> should produce the behavior of a pure lipid system.  Lipids affect each
> other (just like all molecules do).  Headgroup interactions and acyl chain
> packing get more complex with increasing numbers of different lipids.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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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Re: [gmx-users] mdp-settings for charmm36 and lipid apl values

[Justin Lemkul]

On 5/8/13 12:44 PM, Gmx QA wrote:

Thanks Justin, those are good points.

A quick follow up, would you (or someone else) consider the APL-values I
have for my mixed bilayer system to be good, just ok-ish or plain wrong?



I have no basis for making such an assessment, but I know there is literature 
available for 1:1 POPC/POPE membranes that you should look into.  If you want to 
assess accuracy, you need to be working with a well-described system to 
reproduce or one that has experimental information available that you are trying 
to model.


-Justin

--


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Research Scientist
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] Re: Langevin thermostat implementation in GROMACS vs AMBER

[Christoph Junghans]

> Date: Wed, 08 May 2013 16:34:46 +0200
> From: Julian Garrec 
> Subject: Re: [gmx-users] Langevin thermostat implementation in GROMACS
> vs AMBER
> To: Discussion list for GROMACS users 
> Message-ID: <518a6286.8020...@epfl.ch>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> No suggestion ?? :)
>
> In my post I forgot to say that my system contains explicit water.
>
> I'm still very curious about the difference in implementation in AMBER
> and GROMACS. And I still don't really understand the meanning of tau-t
> in LD and how  it is related to other (well defined) quantities such as
> the friction coeficient in equation 3.114 of the manual (v4.6.1).
I am not really sure what your question is, section 7.3.3 is pretty
clear about that:
"the inverse friction constant for each group is set with tau-t", so
gamma_i=1/tau-t, which also makes sense unit-wise as gamma has units
1/ps and tau-t ps

bd-fric is only used for the Brownian dynamics integrator and if
bd-fric=0, the friction is calculated as mass/tau-t. It might be a bit
misleading that bd-fric is listed under section 7.3.4 (Langevin
dynamics), but that stems from the fact that Brownian dynamics is the
overdamped case of stochastic dynamics and hence it is Langevin
Dynamics, too, just in a different limit.

Christoph
>
> Please help,
>
> Sincerely,
>
> Julian
>
>
> Le 04/05/13 13:42, Julian Garrec a 閏rit :
>> Dear all,
>>
>> I am trying to use stochastic dynamics in GROMACS to reproduce some
>> previous results that I got with the AMBER software using the Langevin
>> thermostat.
>>
>> In AMBER, one typically sets what they call the "collision frequency"
>> (noted gamma_ln in the AMBER manual). I typically set gamma_ln to 2
>> collisions per ps (significantly smaller than the internal friction of
>> water, since I use Langevin dynamics as a thermostat).
>>
>> 1) In the mdp options manual, it is recommended to use {integrator=sd
>> ; bd-fric=0 ; tau-t=2}. My understanding is that bd-fric corresponds
>> to 'm_i*gamma_i' in equation 3.114 of the theoretical part of the
>> manual (version 4.6.1). Am I right ?
>>
>> 2) Then, is {integrator=sd ; bd-fric=0 ; tau-t=2} equivalent to
>> {integrator=sd ; bd-fric=0.5} ? (In the theoretical part of the
>> manual, it is said that gamma_i should be set to 0.5 to follow the
>> same spirit).
>>
>> 3) Is 'bd-fric' of GROMACS equivalent to 'gamm_ln' of AMBER ?
>>
>> Thanks for your help,
>>
>> Julian
>>
>
>
> --
> Julian Garrec, research associate
>
> Web: https://sites.google.com/site/juliangarrec/
>
> 蓂uipe : Chimie et Biochimie Th閛riques
> Unit�Mixte de Recherches CNRS UHP 7565
> Universit�de Lorraine, Nancy I BP 239,
> 54506 Vandoeuvre-l鑣-Nancy, cedex France

--
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Web: http://www.compphys.de
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[gmx-users] A problem with do_dssp command

[zugunder]

Hi,

Hi, I have a rather odd problem running do_dssp:

$ do_dssp -h
bash: do_dssp: command not found

I am running GROMACS 4.5.7 under SL 6.3 and everything else seems to work
fine.

DSSP is also installed and should be OK:

$ dssp -h
DSSP 2.0.4 options:
  -h [ --help ] Display help message
  -i [ --input ] argInput file
  -o [ --output ] arg   Output file, use 'stdout' to output to screen
  -v [ --verbose ]  Verbose output
  --version Print version
  -d [ --debug ] argDebug level (for even more verbose output)
..

I am quite confused - is it possible that GROMACS package from EPEL (that I
am using) lacks this program?

Thank you.




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Re: [gmx-users] A problem with do_dssp command

[Justin Lemkul]

On 5/8/13 2:55 PM, zugunder wrote:

Hi,

Hi, I have a rather odd problem running do_dssp:

$ do_dssp -h
bash: do_dssp: command not found

I am running GROMACS 4.5.7 under SL 6.3 and everything else seems to work
fine.

DSSP is also installed and should be OK:

$ dssp -h
DSSP 2.0.4 options:
   -h [ --help ] Display help message
   -i [ --input ] argInput file
   -o [ --output ] arg   Output file, use 'stdout' to output to screen
   -v [ --verbose ]  Verbose output
   --version Print version
   -d [ --debug ] argDebug level (for even more verbose output)
..

I am quite confused - is it possible that GROMACS package from EPEL (that I
am using) lacks this program?



You can check this yourself by investigating the contents of the bin 
subdirectory of wherever Gromacs was installed.  You probably just need to make 
use of GMXRC to configure your environment.


http://www.gromacs.org/Documentation/Installation_Instructions#4.10._Getting_access_to_GROMACS_after_installation

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] Re: A problem with do_dssp command

[zugunder]

Sorry guys, just figured it out:
correct syntax is g_do_dssp :-)

Maybe, it would worth correcting the online manual for GROMACS (which is for
4.6.1 version now)? do_dssp and editconf are mentioned there without "g_"
prefix, unlike many other commands...

Thank you.



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Re: [gmx-users] Re: A problem with do_dssp command

[Justin Lemkul]

On 5/8/13 3:03 PM, zugunder wrote:

Sorry guys, just figured it out:
correct syntax is g_do_dssp :-)

Maybe, it would worth correcting the online manual for GROMACS (which is for
4.6.1 version now)? do_dssp and editconf are mentioned there without "g_"
prefix, unlike many other commands...



Prefixes like these are not standard in Gromacs nomenclature and are a result of 
the way that pre-packaged distributions were created for different operating 
systems.  I believe the Fedora package is the same way.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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[gmx-users] Re: A problem with do_dssp command

[zugunder]

OK, thanks a lot, got it.

But suddenly I got an unexpected error executing do_dssp:

Program g_do_dssp, VERSION 4.5.7
Source code file: /builddir/build/BUILD/gromacs-4.5.7/src/tools/do_dssp.c,
line: 572

Fatal error:
Failed to execute command: /usr/local/bin/dssp -na ddKypQH4 ddgk6w8G >
/dev/null 2> /dev/null

And it gives me a whole bunch of empty or very small files with irregular
names (as those above).

What could this be?



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Re: [gmx-users] Re: A problem with do_dssp command

[Justin Lemkul]

On 5/8/13 3:25 PM, zugunder wrote:

OK, thanks a lot, got it.

But suddenly I got an unexpected error executing do_dssp:

Program g_do_dssp, VERSION 4.5.7
Source code file: /builddir/build/BUILD/gromacs-4.5.7/src/tools/do_dssp.c,
line: 572

Fatal error:
Failed to execute command: /usr/local/bin/dssp -na ddKypQH4 ddgk6w8G >
/dev/null 2> /dev/null

And it gives me a whole bunch of empty or very small files with irregular
names (as those above).

What could this be?



Is the DSSP executable actually located in /usr/local/bin/dssp?  If not, you 
need to set the DSSP environment variable to its actual location (please see the 
Gromacs website where all of this is described).


-Justin

--


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Research Scientist
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] Re: A problem with do_dssp command

[zugunder]

No, it is there:

$ cd /usr/local/bin
[user@localhost bin]$ ls
dssp  vmd

And I had made it executable with chmod a+x

Thank you.



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Re: [gmx-users] Re: Langevin thermostat implementation in GROMACS vs AMBER

[Julian Garrec]

Le 08/05/13 19:33, Christoph Junghans a écrit :

Date: Wed, 08 May 2013 16:34:46 +0200
From: Julian Garrec 
Subject: Re: [gmx-users] Langevin thermostat implementation in GROMACS
 vs AMBER
To: Discussion list for GROMACS users 
Message-ID: <518a6286.8020...@epfl.ch>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

No suggestion ?? :)

In my post I forgot to say that my system contains explicit water.

I'm still very curious about the difference in implementation in AMBER
and GROMACS. And I still don't really understand the meanning of tau-t
in LD and how  it is related to other (well defined) quantities such as
the friction coeficient in equation 3.114 of the manual (v4.6.1).

I am not really sure what your question is, section 7.3.3 is pretty
clear about that:
"the inverse friction constant for each group is set with tau-t", so
gamma_i=1/tau-t, which also makes sense unit-wise as gamma has units
1/ps and tau-t ps

bd-fric is only used for the Brownian dynamics integrator and if
bd-fric=0, the friction is calculated as mass/tau-t. It might be a bit
misleading that bd-fric is listed under section 7.3.4 (Langevin
dynamics), but that stems from the fact that Brownian dynamics is the
overdamped case of stochastic dynamics and hence it is Langevin
Dynamics, too, just in a different limit.

Christoph

Dear Christoph,

Thank you very much for your reply. Actually I am not so much confused 
about the theory :) , but more about how it is implemented, and how this 
implementation differs in GROMACS vs AMBER.


Yes, BD is a limiting case of LD, but still both are implemented with 
different integrators in GROMACS (integrator=sd/bd). From the manual, it 
is clear that both {integrator=bd} and {integrator=bd} can be combined 
with the option bd-fric=0, so I am not so sure that the usage of bd-fric 
is restricted to BD...


Anyway, you are right that it make sense that "gamma_i=1/tau-t", so I 
will keep using {integrator=sd ; bd-fric=0 ; tau-t=XX}.


Many thanks again,

Julian



Please help,

Sincerely,

Julian


Le 04/05/13 13:42, Julian Garrec a 閏rit :

Dear all,

I am trying to use stochastic dynamics in GROMACS to reproduce some
previous results that I got with the AMBER software using the Langevin
thermostat.

In AMBER, one typically sets what they call the "collision frequency"
(noted gamma_ln in the AMBER manual). I typically set gamma_ln to 2
collisions per ps (significantly smaller than the internal friction of
water, since I use Langevin dynamics as a thermostat).

1) In the mdp options manual, it is recommended to use {integrator=sd
; bd-fric=0 ; tau-t=2}. My understanding is that bd-fric corresponds
to 'm_i*gamma_i' in equation 3.114 of the theoretical part of the
manual (version 4.6.1). Am I right ?

2) Then, is {integrator=sd ; bd-fric=0 ; tau-t=2} equivalent to
{integrator=sd ; bd-fric=0.5} ? (In the theoretical part of the
manual, it is said that gamma_i should be set to 0.5 to follow the
same spirit).

3) Is 'bd-fric' of GROMACS equivalent to 'gamm_ln' of AMBER ?

Thanks for your help,

Julian



--
Julian Garrec, research associate

Web: https://sites.google.com/site/juliangarrec/

蓂uipe : Chimie et Biochimie Th閛riques
Unit�Mixte de Recherches CNRS UHP 7565
Universit�de Lorraine, Nancy I BP 239,
54506 Vandoeuvre-l鑣-Nancy, cedex France

--
Christoph Junghans
Web: http://www.compphys.de



--
Julian Garrec, research associate

Web: https://sites.google.com/site/juliangarrec/

Équipe : Chimie et Biochimie Théoriques
Unité Mixte de Recherches CNRS UHP 7565
Université de Lorraine, Nancy I BP 239,
54506 Vandoeuvre-lès-Nancy, cedex France

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[gmx-users] Re: A problem with do_dssp command

[zugunder]

And it seems to me more strange as there is no option "-na" - neither in
dssp, nor in do_dssp.

Or do I missing something? Just in case, here is my command:

$ g_do_dssp -s md_input_extended_to50ns.tpr -f md_product.xtc

where:

.tpr - after I extended the product tun a couple of times
.xtc - unchanged output after the last (extended) production run



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Re: [gmx-users] Re: A problem with do_dssp command

[Justin Lemkul]

On 5/8/13 4:20 PM, zugunder wrote:

And it seems to me more strange as there is no option "-na" - neither in
dssp, nor in do_dssp.

Or do I missing something? Just in case, here is my command:

$ g_do_dssp -s md_input_extended_to50ns.tpr -f md_product.xtc

where:

.tpr - after I extended the product tun a couple of times
.xtc - unchanged output after the last (extended) production run



do_dssp requires a matching version of dssp, which recently had its command-line 
options changed.  Compatibility is toggled with the -ver option of do_dssp.


-Justin

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[gmx-users] Re: A problem with do_dssp command

[zugunder]

Thank you Justin, but I am afraid I do not understand what you mean.

I am using gromacs 4.5.7 and there are no traces of -var option in its
manual (actually, for 4.5.6); moreover, if I try to specify -ver in the
command I get an error on an invalid command line argument. So I suppose,
4.5 can't do that.

How do I know which version of dssp is compatible with do-dssp from gromacs
4.5.7? Should I look for dssp 1.x versions or any of pre-2.0.4 dssp would
work too?

Thank you.




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Re: [gmx-users] Re: A problem with do_dssp command

[Justin Lemkul]

On 5/8/13 5:33 PM, zugunder wrote:

Thank you Justin, but I am afraid I do not understand what you mean.

I am using gromacs 4.5.7 and there are no traces of -var option in its
manual (actually, for 4.5.6); moreover, if I try to specify -ver in the
command I get an error on an invalid command line argument. So I suppose,
4.5 can't do that.

How do I know which version of dssp is compatible with do-dssp from gromacs
4.5.7? Should I look for dssp 1.x versions or any of pre-2.0.4 dssp would
work too?



Perhaps that option was only implemented in the 4.6 series; I thought it was 
backported to the 4.5 branch.  For 4.5, you need a 1.x version of DSSP.  The 2.x 
series is incompatible.  Version 4.6.1 of Gromacs allows you to use either.


-Justin

--


Justin A. Lemkul, Ph.D.
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Department of Biochemistry
Virginia Tech
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[gmx-users] Re: A problem with do_dssp command

[zugunder]

OK, thank you, now it is clear.

So, that's what I've done so far:

1. Got a dsspold binary for Linux (unfortunately, 32bit only).
2. Renamed it into dssp, moved to /usr/local/bin and made it executable with
chmod a+x
3. Because of dsspold being 32bit (giving an error on a wrong ELF
descriptor) I installed 32-bit glibc library.
4. Ran a command, got an xpm output and converted it into .eps with g_xpm2ps
5. The both images are compressed vertically - i.e. Y axis is very short, so
it is not possible to resolve any changes in structure at all.

So I have a question to #5 - did I need to specify any additional
parameters?

Thank you.




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Re: [gmx-users] Re: A problem with do_dssp command

[Justin Lemkul]

On 5/8/13 6:24 PM, zugunder wrote:

OK, thank you, now it is clear.

So, that's what I've done so far:

1. Got a dsspold binary for Linux (unfortunately, 32bit only).
2. Renamed it into dssp, moved to /usr/local/bin and made it executable with
chmod a+x
3. Because of dsspold being 32bit (giving an error on a wrong ELF
descriptor) I installed 32-bit glibc library.
4. Ran a command, got an xpm output and converted it into .eps with g_xpm2ps
5. The both images are compressed vertically - i.e. Y axis is very short, so
it is not possible to resolve any changes in structure at all.

So I have a question to #5 - did I need to specify any additional
parameters?



You can adjust dimensions using an .m2p file.  The online manual has an example.

-Justin

--


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Department of Biochemistry
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[gmx-users] Re: A problem with do_dssp command

[zugunder]

But don't you know where I could find the default settings used in xpm to eps
conversion (without di flag)?
I used the m2p from the example and tried to change some parameters to take
a look what happens, but I can't see any image at all now :-(

Thank you.



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Re: [gmx-users] Re: A problem with do_dssp command

[Justin Lemkul]

On 5/8/13 6:59 PM, zugunder wrote:

But don't you know where I could find the default settings used in xpm to eps
conversion (without di flag)?


The default values simply indicate that each element occupies 1 pixel, such that 
you have some matrix that is N residues by some tens of thousands (maybe) of 
frames, hence why everything is so stretched.  Probably any default settings are 
hard-coded in xpm2ps, but I've never bothered looking for them.



I used the m2p from the example and tried to change some parameters to take
a look what happens, but I can't see any image at all now :-(



Increasing y-size and decrease x-size is appropriate for most DSSP output .xpm 
files, since in general there are many more frames than there are residues in 
the protein.  The difference is typically orders of magnitude.  The example 
online has a nicely annotated description of the parameters.


-Justin

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[gmx-users] mdp-settings for charmm36 and lipid apl values

[Christopher Neale]

It is a really bad idea to use standard tip3p with charmm36 lipids (see the 
Piggot paper that you referenced and also Sapay, N. et al. 2010 J. Comp. Chem. 
32, 1400-1410 + probably others).

dt 0.001 with nstlist 5 seems like overkill on the nstlist update frequency 
(not a problem though).

Here's how I do charmm36 lipid simulations:

constraints = all-bonds
lincs-iter =  1
lincs-order =  6
constraint_algorithm =  lincs
integrator = sd
dt = 0.002
tinit = 0
nsteps = 500
nstcomm = 1
nstxout = 500
nstvout = 500
nstfout = 500
nstxtcout = 5
nstenergy = 5
nstlist = 10
nstlog=0 ; reduce log file size
ns_type = grid
vdwtype = switch
rlist = 1.2
rlistlong = 1.3
rvdw = 1.2
rvdw-switch = 0.8
rcoulomb = 1.2
coulombtype = PME
ewald-rtol = 1e-5
optimize_fft = yes
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
tc_grps =  System
tau_t   =  1.0
ld_seed =  -1
ref_t = 310
gen_temp = 310
gen_vel = yes
unconstrained_start = no
gen_seed = -1
Pcoupl = berendsen
pcoupltype = semiisotropic
tau_p = 4 4
compressibility = 4.5e-5 4.5e-5
ref_p = 1.0 1.0


For a pure POPC bilayer with Charmm36 lipids and tips3p water, I get ~ 0.64 
nm^2/lipid (not using grid-mat, just looking at box dimensions).

If I use regular tip3p instead, the APL decreases a lot and eventually forms a 
gel. In simple terms of APL and phase, you can get the same results as tips3p 
(0.64 nm^2/lipid) if you use tip4p (and spce is not too bad, but is still not 
as close as tip4p). Note tip4p will run faster than tips3p by a large margin. 
Nevertheless, I use tip3sp in all of my work with charmm36. 

Also, note that ions can shrink your APL, particularly Na+ (and divalent 
cations are even worse). My simulations use 50 mM KCl, which basically doesn't 
affect the average APL (although 50 mM NaCl does noticeably reduce the APL).

Finally, I am not convinced that a per-molecule area per lipid is a useful 
quantity to compare to experimental areas per lipid. I haven't looked at 
Grid-Mat myself, but there must be a lot of assumptions underlying any analysis 
that tried to assign an "area" to a single 3D lipid. If I were you, I'd be 
looking for expt. results of APL for POPC vs. POPE vs. 70%POPC/30%POPE. Also, 
are you entirely sure that you didn't mix up the POPC vs. POPE values? It looks 
to me like a simple labelling error enough that it warrants a second look.

Chris.



-- original message --

I've been experimenting with simulations of mixed bilayers (512 lipids in
total, 70% POPC, 30% POPE) using the charmm36 parameter set in gromacs, and
have a couple of questions. I know this has been discussed before, but I'd
appreciate some input nonetheless :-)

The relevant sections of my mdp-file are pasted below:

; Start time and timestep in ps
tinit= 0
dt   = 0.001
nsteps   = 1

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist  = 5
; ns algorithm (simple or grid)
ns_type  = grid
; Periodic boundary conditions: xyz, no, xy
pbc  = xyz
periodic_molecules   = no
; nblist cut-off
rlist= 1.2
; long-range cut-off for switched potentials
rlistlong= 1.4

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = PME
rcoulomb-switch  = 0
rcoulomb = 1.2
; Relative dielectric constant for the medium and the reaction field
epsilon_r= 1
epsilon_rf   = 1
; Method for doing Van der Waals
vdw-type = switch
; cut-off lengths
rvdw-switch  = 0.8
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = No

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
tcoupl   = V-rescale
nsttcouple   = -1
nh-chain-length  = 10
; Groups to couple separately
tc-grps  = System
; Time constant (ps) and reference temperature (K)
tau_t= 0.1
ref_t= 300
; Pressure coupling
pcoupl   = Parrinello-Rahman
pcoupltype   = semiisotropic
nstpcouple   = -1

This is as far as I can tell from earlier discussions on the list, and also
from reading the Piggott et al. paper in JCTC, the correct settings for
charmm36.

After a simulation of ~50 ns, I use GridMatMD to calculate the area per
headgroup of POPC and POPE, respectively, and get what I think are not 100%
acceptable results (but maybe they are)

For POPC, I get 59,7 A^2, and for POPE, I get 63,1 A^2.

The value for POPE would have been fine I suppose if it hadn't been for the
fact that the APL for POPC is smaller. Should it not be larger than POPE?

I notice in the Piggott-paper that they in the supplement for some
simulations of POPC also get APL's of around 59-60 (without POPE of
c

[gmx-users] Re: A problem with do_dssp command

[zugunder]

May I ask you to share the content of your m2p?

The problem here is that using defaults (no -di) I at least can see some eps
image via evince for example, but when I use m2p consisting of these 2
lines:

xbox = 0.2  ; x-size of a matrix element
ybox = 20.0 ; y-size of a matrix element

I don't see any image, moreover, evince hangs up.

However, as it turned out, .xpm is easily viewable and editable with Gimp...
that's probably even more convenient.



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Re: [gmx-users] Re: A problem with do_dssp command

[Justin Lemkul]

On 5/8/13 7:18 PM, zugunder wrote:

May I ask you to share the content of your m2p?



The size of the matrix elements is subjective; it depends on what dimensions of 
the matrix you want.  My usual settings are xbox = 0.05, ybox = 2.0, but that's 
for my systems, which are relatively small along y.



The problem here is that using defaults (no -di) I at least can see some eps
image via evince for example, but when I use m2p consisting of these 2
lines:

xbox = 0.2  ; x-size of a matrix element
ybox = 20.0 ; y-size of a matrix element

I don't see any image, moreover, evince hangs up.

However, as it turned out, .xpm is easily viewable and editable with Gimp...
that's probably even more convenient.



Could be.  As I recall, you don't get all the legend information if you open the 
.xpm directly, though.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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[gmx-users] keeping water (entirely) out of the bilayer core

[Christopher Neale]

Dear Jianguo, XAvier, and Dallas:

Thank you for your great suggestions. I am making progress, but still have not 
found an efficient way
to do this. I don;t have any particular questions in this post, but wanted to 
provide an update and
also to see if anybody has any additional ideas based on what I have tried.

Jianguo: I have successfully interfaced plumed with gromacs and was able to do 
what I wanted. 
My initial (naive) approach is inefficient (speed reduced from 26 ns/day to 1.7 
ns.day) although I 
am getting some help from the plumed developers to find a more efficient 
approach.

XAvier: I was unable to find a repulsive potential that I could apply to water 
molecules, excepting 
simply increasing the LJ repulsion. I suspect that this approach is not going 
to work for me since the 
lipid-water interface is rugged and lipid tails sometimes approach the surface 
and, therefore, 
a LJ repulsion approach might end up creating large vaccuums at the interfacial 
region.

Dallas and Jianguo: This might work. I would need to find a way to anchor 
virtual atoms at the bilayer center.
Unfortunately, other parts of my approach make it undesirable to have an r^12 
(LJ) or exponential (Buckingham)
repulsion. Specifically, I'd like to be able to not only keep water molecules 
out of the bilayer core
but also force them out if they are already inside, and these rapidly rising 
potentials will likely lead
to expolding systems if water molecules are already deeply burried in the 
bilayer core. However, there might 
be a way forward with the free energy code using some type of soft core 
potential on the LJ via the 
free energy code. I'm going to try this and will report back.

Also, I did get gromacs to do this with the following 2 code changes in 
src/mdlib/pull.c:

(i) in static void do_pull_pot(), immediately after calling 
get_pullgrp_distance(), I
added the following code
if(g>1&&dev[0]>0.0){
dev[0]=0.0;
}

When used with ePull == epullUMBRELLA and pull->eGeom == epullgDIST, this 
ensures that the pull force only
contributes when the displacement is smaller than the reference distance, but 
is not applied when
the displacement is larger than the reference distance.

(ii) I removed the following code from get_pullgrps_dr():

if (max_dist2 >= 0 && dr2 > 0.98*0.98*max_dist2)
{
gmx_fatal(FARGS, "Distance of pull group %d (%f nm) is larger than 0.49 
times the box size (%f)", g, sqrt(dr2), sqrt(max_dist2));
}

Normally, I suppose that this code is there so that atoms are not being pulled 
in oscillating directions when
they are 1/2 box dimension away from the reference position (although I am not 
exactly sure why that would
be an error). Nevertheless, this error is not necessary in my case because I 
have also removed any force when atoms are farther away than the reference 
distance (in modificaion i, above).

After making these modification, I then added about 10,000 separate pull 
groups, one for each water oxygen 
atom, each of which keeps that water molecule out of the bilayer core along Z.

The only problem with this approach is that it is really inefficient: with 16 
threads over 8 cores, I get 
26 ns/day without the 10,000 pull groups and only 4 ns/day with the pull 
groups, probably because so much 
information is being passed around between threads for the water molecules that 
are really far away from
the bilayer center.

Thank you,
Chris.

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[gmx-users] Re: mdrun-gpu error message on Gromacs 4.5.5

[Andrew DeYoung]

Hi Justin,

Thank you so much.  We were trying to use version 4.5.5 with OpenMM because
I was silly.  I mistakenly thought 4.6.x was in beta, but apparently I did
not read the release page: 4.6.1 has been out for some time now. 

Version 4.6.1 has made our GPU lives a lot easier.  Thank you so, so much
for your help! 

Andrew DeYoung
Carnegie Mellon University

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[gmx-users] error after grompp

[Nur Syafiqah Abdul Ghani]

Hi all,

I need to do simulation which same as protein-ligand tutorial by Justin.
The different is i'm using my protein and the ligand was zinc.
I already follow everything in that tutorial and suddenly when i want
to heat my protein by using the nvt.mdp there was an error state like
below :

Fatal error:
Atom 410 in multiple T-Coupling groups (1 and 2)

Actually I do not understand what the error said even when i'm Google
it to forum there was no one
facing like mine..Here i put together my topology and the nvt.mdp.
Hope you can give me some idea that i cant see.

Another question,why is in the nvt.mdp at the temperature coupling
there were twice of 300 of tcoupl and also the tau_t : 01. 01. Can u
explain it why?

topology :

; Include forcefield parameters
#include "gromos53a6.ff/forcefield.itp"

; Include chain topologies
#include "metal_Protein_chain_A.itp"

; Include position restraint for protein
#ifdef POSRES
#include "posre_Protein_chain_A.itp"
#endif

; Include ion chain topologies
#include "metal_Ion_chain_A2.itp"

; Include position restraint for metal
#ifdef POSRES_ION
#include "posre_Ion_chain_A2.itp"
#endif

; Include water topology
#include "gromos53a6.ff/spc.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

; Include topology for ions
#include "gromos53a6.ff/ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound#mols
Protein_chain_A 1
Ion_chain_A21
SOL 8780
NA   1


nvt.mdp :

title   = Protein-ligand complex NVT equilibration
cpp = /usr/bin/cpp
include = -I/usr/share/gromacs/top
define  = -DPOSRES  ; position restrain the protein and ligand
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 5 ; 2 * 5 = 100 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 100   ; save coordinates every 0.2 ps
nstvout = 100   ; save velocities every 0.2 ps
nstenergy   = 100   ; save energies every 0.2 ps
nstlog  = 100   ; update log file every 0.2 ps
energygrps  = Protein ZN
; Bond parameters
continuation= no; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cells
nstlist = 10; 10 fs
rlist   = 1.4   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.4   ; short-range electrostatic cutoff (in nm)
rvdw= 1.4   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling
tcoupl  = V-rescale ; modified Berendsen thermostat
tc-grps = Protein_ZN Water_and_ions; two coupling groups - more accurate
tau_t   = 0.1 0.1 ; time constant, in ps
ref_t   = 300 300 ; reference temperature, one
for each group, in K
; Pressure coupling
pcoupl  = no; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; assign velocities from Maxwell distribution
gen_temp= 300   ; temperature for Maxwell distribution
gen_seed= -1; generate a random seed






Thanks for your help in advance,

Nur Syafiqah Abdul Ghani,
Theoretical and Computational Chemistry Laboratory,
Department of Chemistry,
Faculty of Science,
Universiti Putra Malaysia,
43400 Serdang,
Selangor.
alternative email : syafiqahabdulgh...@gmail.com @ gs33...@mutiara.upm.edu.my
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