[gmx-users] using recolor.sh to color the xpm matrix files produced by r_rms and g_mdmat

[Hassan Shallal]

Dear Gromacs users,
 
I have been trying to use the recolor.sh mentioned in this wbsite 
http://nmr.chem.uu.nl/~tsjerk/course/molmod/analysis1.html 
 
to reclor an xpm file called rmsd-matrix.xpm file, whenever I issue the command 
recolor.sh rmsd-matrix.xpm, I get the following error message:
 
#$ hassan~ $./recolor.sh rmsd-matrix.xpm
GIMP-Error: Opening '/home/hshallal/(gimp-file-save 1 1 2 "./rmsd-matrix.png" 
"./rmsd-matrix.png")' failed: No such file or directory
GIMP-Error: Opening '/home/hshallal/(gimp-quit 0)' failed: No such file or 
directory
batch command: executed successfully

It seems like a problem with gimp not being able to process as stated in the 
script, especially with the argument of "(gimp-file-save 1 1 2 \"$png\" 
\"$png\")" (look below for the contents of the script).  

I have gimp confidured in my system. has anyone ran across the same problem or 
can know what the problem is and what th solution might be?

Thanks in advance

Hassan

The contents of the recolor.sh file:

#!/bin/sh

xpm=$1
png=`dirname $xpm`/`basename $xpm .xpm`.png
convert xc:red xc:orange xc:yellow xc:green1 xc:cyan xc:blue xc:magenta \
  +append -filter Cubic -resize 600x30\! -rotate 90 gradient_rainbow.jpg
#convert -size 1x600 xc:'#0C0' -colorspace HSB \
#  gradient: -compose CopyRed -composite \
#  -colorspace RGB gradient_rainbow.jpg
gimp -d -f -i -b "(gimp-file-load 1 \"$xpm\" \"$xpm\")" "(gimp-file-save 1 1 2 
\"$png\" \"$png\")" "(gimp-quit 0)"
convert $png gradient_rainbow.jpg -virtual-pixel edge -fx 'v.p{0,u*v.h}' $png

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Re: [gmx-users] NMA

[Justin A. Lemkul]

Yao Yao wrote:

HI Gmxers,

Anyone came across a step-by-step tutorial for normal mode analysis, not a
theoretical background introduction but a practical hands-on demonstration in
gromacs? I dunno what steps to follow.



http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis

-Justin


Thanks,

Yao





--


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] NMA

[Yao Yao]

HI Gmxers,

Anyone came across a step-by-step tutorial for normal mode analysis, not a 
theoretical background introduction but a practical hands-on demonstration in 
gromacs? I dunno what steps to follow. 

Thanks,

Yao


  
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[gmx-users] Com Pulling

[chris . neale]

I understand your intention now. It might be possible to do this with  
gromacs 3.3.3 (short pull code simulation, then restart without the  
pull code but using the .trr from the previous run) but I'm not sure  
if you can do that with 4.x. Note that a thermostat is going to remove  
this directed velocity over time.


You can put velocities into a .gro file .. I presume that these are  
used if you set gen_vel=no, but I'm not sure about that. Test that by  
loading in a .gro with velocities and set gen_vel=no and nstep=0 and  
see if you have an instantaneous temperature near 300K or near 0K. If  
it works, then you can write a script or program to set your own  
initial velocities this way.


Chris.

-- original message --

Dear Chris Neale,

I wanted to generate directed initial velocities for two seperate  
multiprotein complexes, but just so they start to move through the  
void towards each other.  The only way I found to do this was to use  
the COM pulling, but then it is a "biasing" force applied across the  
entire MD sim.  Basically I want to minimize the bias, if possible,  
but was asking if there is a way to apply an initial directional  
(instead of the random)velocity/force without a constant applied force  
like the COM pulling.  If it is the only way, I can do the  
calculations with COM pulling and correct for my applied force, but  
was hopeing there was another way I did not find which would be more  
simple, or just something I missed.


In Solvent, the complexes move (albeit random), and one only need to  
let it run long enough, or apply walls, but in vacuo if there is no  
applied force, the atoms within the complexes move around, but not the  
molecules as a whole, they just sit waving at each other across a void.


As they are in a void however, an initial force would not dissapate  
until the two larger molecules connected, so I am woundering if there  
would even be a difference between what I wanted, and general COM  
pulling.


reguardless,thanks for any reply.

Sincerely,

Stephan Watkins

--

Message: 4
Date: Wed, 15 Dec 2010 11:04:12 -0500
From: chris.neale at utoronto.ca
Subject: [gmx-users] Com Pulling
To: gmx-users at gromacs.org
Message-ID: <20101215110412.imqto29twk8ksk80 at webmail.utoronto.ca>
Content-Type: text/plain;charset=ISO-8859-1;DelSp="Yes";
format="flowed"

If I understand correctly, you want to apply a biasing force and you
also want to have an "unbiased" simulation. These two things are not
possible in combination. There are a variety of techniques available
that will give you particular information. For example, you can
extract the unbiased PMF from umbrella sampling (but not the unbiased
dynamics); you can also study some things with reaction path sampling
or slow AFM pulling, but for us to help you you will need to describe
what you want to do.

Chris.

-- original message --

Dear All,

I was setting up things to use COM pulling for a multiprotein complex.
  My question after going through the gromacs documentation(online) is:

Is there a way to limit either the time or distance two groups are
pulled towards each other(reguarding only the applied force), as I
could not find anything.  Basically, if I run something in vacuo, the
groups (proteins) do not move globally even when constraints, etc are
set to none.  To measure any Gibbs , delta H etc...I need the groups
too move towards each other and form the interactions I am measuring,
but do not want the pull force to interfear with overall calculations.

My thoughts were to do a very short run, and then either remove the
pull force, etc from the .mdp file, and use a checkpoint to re-start
it, but do not know if this would work or would maintain the movement
however arbitrary in the general correct direction.

that or use such a small (.2 kcal/mol nm2) that it does not matter very much.

Sincerely,

Stephan Watkins
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[gmx-users] Re: RE:Com Pulling

[lloyd riggs]

Dear Chris Neale,

I wanted to generate directed initial velocities for two seperate multiprotein 
complexes, but just so they start to move through the void towards each other.  
The only way I found to do this was to use the COM pulling, but then it is a 
"biasing" force applied across the entire MD sim.  Basically I want to minimize 
the bias, if possible, but was asking if there is a way to apply an initial 
directional (instead of the random)velocity/force without a constant applied 
force like the COM pulling.  If it is the only way, I can do the calculations 
with COM pulling and correct for my applied force, but was hopeing there was 
another way I did not find which would be more simple, or just something I 
missed.

In Solvent, the complexes move (albeit random), and one only need to let it run 
long enough, or apply walls, but in vacuo if there is no applied force, the 
atoms within the complexes move around, but not the molecules as a whole, they 
just sit waving at each other across a void.

As they are in a void however, an initial force would not dissapate until the 
two larger molecules connected, so I am woundering if there would even be a 
difference between what I wanted, and general COM pulling.

reguardless,thanks for any reply.

Sincerely,

Stephan Watkins

--

Message: 4
Date: Wed, 15 Dec 2010 11:04:12 -0500
From: chris.ne...@utoronto.ca
Subject: [gmx-users] Com Pulling
To: gmx-users@gromacs.org
Message-ID: <20101215110412.imqto29twk8ks...@webmail.utoronto.ca>
Content-Type: text/plain;charset=ISO-8859-1;DelSp="Yes";
format="flowed"

If I understand correctly, you want to apply a biasing force and you  
also want to have an "unbiased" simulation. These two things are not  
possible in combination. There are a variety of techniques available  
that will give you particular information. For example, you can  
extract the unbiased PMF from umbrella sampling (but not the unbiased  
dynamics); you can also study some things with reaction path sampling  
or slow AFM pulling, but for us to help you you will need to describe  
what you want to do.

Chris.

-- original message --

Dear All,

I was setting up things to use COM pulling for a multiprotein complex.  
  My question after going through the gromacs documentation(online) is:

Is there a way to limit either the time or distance two groups are  
pulled towards each other(reguarding only the applied force), as I  
could not find anything.  Basically, if I run something in vacuo, the  
groups (proteins) do not move globally even when constraints, etc are  
set to none.  To measure any Gibbs , delta H etc...I need the groups  
too move towards each other and form the interactions I am measuring,  
but do not want the pull force to interfear with overall calculations.

My thoughts were to do a very short run, and then either remove the  
pull force, etc from the .mdp file, and use a checkpoint to re-start  
it, but do not know if this would work or would maintain the movement  
however arbitrary in the general correct direction.

that or use such a small (.2 kcal/mol nm2) that it does not matter very much.

Sincerely,

Stephan Watkins
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Re: Antw: [gmx-users] NaN error using mdrun-gpu

[Bongkeun Kim]

Hello,

This is the output from deviceQuery command:
./deviceQuery Starting...

 CUDA Device Query (Runtime API) version (CUDART static linking)

There are 4 devices supporting CUDA

Device 0: "Tesla T10 Processor"
  CUDA Driver Version:   3.20
  CUDA Runtime Version:  3.20
  CUDA Capability Major revision number: 1
  CUDA Capability Minor revision number: 3
  Total amount of global memory: 4294770688 bytes
  Number of multiprocessors: 30
  Number of cores:   240
  Total amount of constant memory:   65536 bytes
  Total amount of shared memory per block:   16384 bytes
  Total number of registers available per block: 16384
  Warp size: 32
  Maximum number of threads per block:   512
  Maximum sizes of each dimension of a block:512 x 512 x 64
  Maximum sizes of each dimension of a grid: 65535 x 65535 x 1
  Maximum memory pitch:  2147483647 bytes
  Texture alignment: 256 bytes
  Clock rate:1.44 GHz
  Concurrent copy and execution: Yes
  Run time limit on kernels: No
  Integrated:No
  Support host page-locked memory mapping:   Yes
  Compute mode:  Default (multiple  
host threads can use this device simultaneously)


Device 1: "Tesla T10 Processor"
  CUDA Driver Version:   3.20
  CUDA Runtime Version:  3.20
  CUDA Capability Major revision number: 1
  CUDA Capability Minor revision number: 3
  Total amount of global memory: 4294770688 bytes
  Number of multiprocessors: 30
  Number of cores:   240
  Total amount of constant memory:   65536 bytes
  Total amount of shared memory per block:   16384 bytes
  Total number of registers available per block: 16384
  Warp size: 32
  Maximum number of threads per block:   512
  Maximum sizes of each dimension of a block:512 x 512 x 64
  Maximum sizes of each dimension of a grid: 65535 x 65535 x 1
  Maximum memory pitch:  2147483647 bytes
  Texture alignment: 256 bytes
  Clock rate:1.44 GHz
  Concurrent copy and execution: Yes
  Run time limit on kernels: No
  Integrated:No
  Support host page-locked memory mapping:   Yes
  Compute mode:  Default (multiple  
host threads can use this device simultaneously)


Device 2: "Tesla T10 Processor"
  CUDA Driver Version:   3.20
  CUDA Runtime Version:  3.20
  CUDA Capability Major revision number: 1
  CUDA Capability Minor revision number: 3
  Total amount of global memory: 4294770688 bytes
  Number of multiprocessors: 30
  Number of cores:   240
  Total amount of constant memory:   65536 bytes
  Total amount of shared memory per block:   16384 bytes
  Total number of registers available per block: 16384
  Warp size: 32
  Maximum number of threads per block:   512
  Maximum sizes of each dimension of a block:512 x 512 x 64
  Maximum sizes of each dimension of a grid: 65535 x 65535 x 1
  Maximum memory pitch:  2147483647 bytes
  Texture alignment: 256 bytes
  Clock rate:1.44 GHz
  Concurrent copy and execution: Yes
  Run time limit on kernels: No
  Integrated:No
  Support host page-locked memory mapping:   Yes
  Compute mode:  Default (multiple  
host threads can use this device simultaneously)


Device 3: "Tesla T10 Processor"
  CUDA Driver Version:   3.20
  CUDA Runtime Version:  3.20
  CUDA Capability Major revision number: 1
  CUDA Capability Minor revision number: 3
  Total amount of global memory: 4294770688 bytes
  Number of multiprocessors: 30
  Number of cores:   240
  Total amount of constant memory:   65536 bytes
  Total amount of shared memory per block:   16384 bytes
  Total number of registers available per block: 16384
  Warp size: 32
  Maximum number of threads per block:   512
  Maximum sizes of each dimension of a block:512 x 512 x 64
  Maximum sizes of each dimension of a 

Re: [gmx-users] How to define Center of Mass velocity of a specific group

[Justin A. Lemkul]

Tomy van Batis wrote:



On Tue, Dec 14, 2010 at 2:19 PM, Justin A. Lemkul > wrote:




Tomy van Batis wrote:

Dear all

I have a system consisting of 2 substrates (20 nm distance
between them) and inside them there are polymer chains. I would
like during my NVT simulations the substrates NOT to move (I
suppose I have to put  the velocity of the COM of it's substrate
to be zero).

Does anyone know how to do that?


The simplest way is to just use position restraints.  The positions
may change very slightly, but not a noticeable amount.

If you absolutely require no movement at all, use freezegrps in the
.mdp file.

-Justin

Thanks in advance
Chrysostomos 


Dear Justin

I found how to freeze the group that I want, but what I can't find is 
how to use the position restrains.


I created just 1 chain. As I can see in my* topol.top* file it's 
automatically included the *posre.itp* file. I inserted in my *.mdp* 
file the following line:

 define = -DPOSRE

but after running NVT for few steps I see that the chain is still moving 
a lot.


I can't find any example in the manual or in the internet. Can you 
please tell me what to do?




If the topology was written by pdb2gmx, the #define statement should be "#define 
POSRES," not "#define POSRE," so your define statement in the .mdp file is 
incorrect.


-Justin


Many thanks

Chrysostomos



--


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] pullx.xvg / pullf.xvg

[chris . neale]

please copy and paste your commands your output. It is unlikely that  
any of us are going to do that tutorial in order to understand your  
question.


-- original message --

Hi,

I am following the umbrella sampling tutorial written by Justin Lemkul.

I was successfully able to run the umbrella sampling simulations, but  
for each configuration it outputted a single xvg file.


For the data analysis i should have pullf.xvg / pullx.xvg filesbut  
these files are not outputted after the simulation run.


I haven't made any changes to the .mdp files mentioned in the tutorial.


Please can i know what might have gone wrong that it has not produced  
pullf.xvg and pullx.xvg files.




Kind regards,
chetan.


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[gmx-users] Com Pulling

[chris . neale]

If I understand correctly, you want to apply a biasing force and you  
also want to have an "unbiased" simulation. These two things are not  
possible in combination. There are a variety of techniques available  
that will give you particular information. For example, you can  
extract the unbiased PMF from umbrella sampling (but not the unbiased  
dynamics); you can also study some things with reaction path sampling  
or slow AFM pulling, but for us to help you you will need to describe  
what you want to do.


Chris.

-- original message --

Dear All,

I was setting up things to use COM pulling for a multiprotein complex.  
 My question after going through the gromacs documentation(online) is:


Is there a way to limit either the time or distance two groups are  
pulled towards each other(reguarding only the applied force), as I  
could not find anything.  Basically, if I run something in vacuo, the  
groups (proteins) do not move globally even when constraints, etc are  
set to none.  To measure any Gibbs , delta H etc...I need the groups  
too move towards each other and form the interactions I am measuring,  
but do not want the pull force to interfear with overall calculations.


My thoughts were to do a very short run, and then either remove the  
pull force, etc from the .mdp file, and use a checkpoint to re-start  
it, but do not know if this would work or would maintain the movement  
however arbitrary in the general correct direction.


that or use such a small (.2 kcal/mol nm2) that it does not matter very much.

Sincerely,

Stephan Watkins
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Re: [gmx-users] Question about Extention simulation in REMD

[Justin A. Lemkul]

Qin Qiao wrote:

Dear Sir or Madam,

I wonder how to continue a REMD running using .cpt file in Gromacs 
4.5.1. Since I ran a REMD of 56 replicas, there are one cpt file for 
each replica.. I couldn't do it by


tpbconv -s previous.tpr -extend timetoextendby -o next.tpr

mdrun -s next.tpr -cpi previous.cpt


I guess it's not for an iterative line in the answer in 
http://www.mail-archive.com/gmx-users@gromacs.org/msg33566.html, since 
the mdrun should run simultaneously.




The iterative approach Mark describes in that post is for the tpbconv step. 
Simply extend all of your .tpr files to generate new ones (iterate over all your 
.tpr files), then proceed with mdrun as you would normally, making use of the 
-cpi feature.


-Justin


Could you give some advice? Thanks.

Best,

Qin



--


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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Re: [gmx-users] RE: Log files

[Justin A. Lemkul]

Nimesh Jain wrote:

How do I turn off md.log fine generation in Gromacs?


You can probably just set nstlog = 0 in the .mdp file.

-Justin



Thanks



--


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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Re: Antw: [gmx-users] NaN error using mdrun-gpu

[Justin A. Lemkul]

Bongkeun Kim wrote:

Hello,

I tried using 1fs timestep and it did not work.
I'm using nvidia T10 gpus(c1060 or s1070) and mdrun-gpu said it's not 
supported gpu and I had to use "force-device=y". Do you think this is 
the reason of the error?


Probably.  Please note the documentation and the specific warning about this 
option:

http://www.gromacs.org/Downloads/Installation_Instructions/Gromacs_on_GPUs?highlight=gromacs+on+gpu#Gromacs-GPU_specific_mdrun_features

Also, when using PME, I don't think there's any real benefit to using the GPU 
version of mdrun.  I seem to recall posts that doing so actually results in 
poorer performance than the standard CPU binary.  GPU is particularly beneficial 
for implicit solvent simulations.


-Justin


Thanks.
Bongkeun Kim

Quoting Emanuel Peter :


Hello,

If you use for your timestep 1fs instead of 2fs, it could run better.

Bests,

Emanuel


Bongkeun Kim  15.12.10 8.36 Uhr >>>

Hello,



I got an error log when I used gromacs-gpu on npt simulation.

The error is like:

---

Input Parameters:

integrator   = md

nsteps   = 5000

init_step= 0

ns_type  = Grid

nstlist  = 5

ndelta   = 2

nstcomm  = 10

comm_mode= Linear

nstlog   = 1000

nstxout  = 1000

nstvout  = 1000

nstfout  = 0

nstcalcenergy= 5

nstenergy= 1000

nstxtcout= 1000

init_t   = 0

delta_t  = 0.002

xtcprec  = 1000

nkx  = 32

nky  = 32

nkz  = 32

pme_order= 4

ewald_rtol   = 1e-05

ewald_geometry   = 0

epsilon_surface  = 0

optimize_fft = FALSE

ePBC = xyz

bPeriodicMols= FALSE

bContinuation= TRUE

bShakeSOR= FALSE

etc  = V-rescale

nsttcouple   = 5

epc  = Parrinello-Rahman

epctype  = Isotropic

nstpcouple   = 5

tau_p= 2

ref_p (3x3):

   ref_p[0]={ 1.0e+00,  0.0e+00,  0.0e+00}

   ref_p[1]={ 0.0e+00,  1.0e+00,  0.0e+00}

   ref_p[2]={ 0.0e+00,  0.0e+00,  1.0e+00}

compress (3x3):

   compress[0]={ 4.5e-05,  0.0e+00,  0.0e+00}

   compress[1]={ 0.0e+00,  4.5e-05,  0.0e+00}

   compress[2]={ 0.0e+00,  0.0e+00,  4.5e-05}

refcoord_scaling = No

posres_com (3):

   posres_com[0]= 0.0e+00

   posres_com[1]= 0.0e+00

   posres_com[2]= 0.0e+00

posres_comB (3):

   posres_comB[0]= 0.0e+00

   posres_comB[1]= 0.0e+00

   posres_comB[2]= 0.0e+00

andersen_seed= 815131

rlist= 1

rlistlong= 1

rtpi = 0.05

coulombtype  = PME

rcoulomb_switch  = 0

rcoulomb = 1

vdwtype  = Cut-off

rvdw_switch  = 0

rvdw = 1

epsilon_r= 1

epsilon_rf   = 1

tabext   = 1

implicit_solvent = No

gb_algorithm = Still

gb_epsilon_solvent   = 80

nstgbradii   = 1

rgbradii = 1

gb_saltconc  = 0

gb_obc_alpha = 1

gb_obc_beta  = 0.8

gb_obc_gamma = 4.85

gb_dielectric_offset = 0.009

sa_algorithm = Ace-approximation

sa_surface_tension   = 2.05016

DispCorr = EnerPres

free_energy  = no

init_lambda  = 0

delta_lambda = 0

n_foreign_lambda = 0

sc_alpha = 0

sc_power = 0

sc_sigma = 0.3

sc_sigma_min = 0.3

nstdhdl  = 10

separate_dhdl_file   = yes

dhdl_derivatives = yes

dh_hist_size = 0

dh_hist_spacing  = 0.1

nwall= 0

wall_type= 9-3

wall_atomtype[0] = -1

wall_atomtype[1] = -1

wall_density[0]  = 0

wall_density[1]  = 0

wall_ewald_zfac  = 3

pull = no

disre= No

disre_weighting  = Conservative

disre_mixed  = FALSE

dr_fc= 1000

dr_tau   = 0

nstdisreout  = 100

orires_fc= 0

orires_tau   = 0

nstorireout  = 100

dihre-fc = 1000

em_stepsize  = 0.01

em_tol   = 10

niter= 20

fc_stepsize  = 0

nstcgsteep   = 1000

nbfgscorr 

[gmx-users] Re: Com Pulling

[lloyd riggs]

Dear All,

I was setting up things to use COM pulling for a multiprotein complex.  My 
question after going through the gromacs documentation(online) is:

Is there a way to limit either the time or distance two groups are pulled 
towards each other(reguarding only the applied force), as I could not find 
anything.  Basically, if I run something in vacuo, the groups (proteins) do not 
move globally even when constraints, etc are set to none.  To measure any Gibbs 
, delta H etc...I need the groups too move towards each other and form the 
interactions I am measuring, but do not want the pull force to interfear with 
overall calculations.

My thoughts were to do a very short run, and then either remove the pull force, 
etc from the .mdp file, and use a checkpoint to re-start it, but do not know if 
this would work or would maintain the movement however arbitrary in the general 
correct direction.

that or use such a small (.2 kcal/mol nm2) that it does not matter very much.

Sincerely,

Stephan Watkins
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Re: [gmx-users] RE: Log files

[Javier Cerezo]

I don't think you can turn out log file generation (note that it's not 
an optional output). If you don't want to write intermediate steps in 
this file you can set:

nstlog = 0
in your mdp file. In any case, the first and last step will be written.

Javier

El 15/12/10 16:20, Nimesh Jain escribió:

How do I turn off md.log fine generation in Gromacs?

Thanks


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Re: [gmx-users] How to define Center of Mass velocity of a specific group

[Tomy van Batis]

On Tue, Dec 14, 2010 at 2:19 PM, Justin A. Lemkul  wrote:

>
>
> Tomy van Batis wrote:
>
>> Dear all
>>
>> I have a system consisting of 2 substrates (20 nm distance between them)
>> and inside them there are polymer chains. I would like during my NVT
>> simulations the substrates NOT to move (I suppose I have to put  the
>> velocity of the COM of it's substrate to be zero).
>>
>> Does anyone know how to do that?
>>
>
> The simplest way is to just use position restraints.  The positions may
> change very slightly, but not a noticeable amount.
>
> If you absolutely require no movement at all, use freezegrps in the .mdp
> file.
>
> -Justin
>
>  Thanks in advance
>> Chrysostomos 
>>
>>
Dear Justin

I found how to freeze the group that I want, but what I can't find is how to
use the position restrains.

I created just 1 chain. As I can see in my* topol.top* file it's
automatically included the *posre.itp* file. I inserted in my *.mdp* file
the following line:
 define = -DPOSRE

but after running NVT for few steps I see that the chain is still moving a
lot.

I can't find any example in the manual or in the internet. Can you please
tell me what to do?

Many thanks

Chrysostomos
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[gmx-users] RE: Log files

[Nimesh Jain]

How do I turn off md.log fine generation in Gromacs?

Thanks
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[gmx-users] pullx.xvg / pullf.xvg

[Poojari, Chetan]

Hi,

I am following the umbrella sampling tutorial written by Justin Lemkul.

I was successfully able to run the umbrella sampling simulations, but for each 
configuration it outputted a single xvg file.

For the data analysis i should have pullf.xvg / pullx.xvg filesbut these 
files are not outputted after the simulation run.

I haven't made any changes to the .mdp files mentioned in the tutorial.


Please can i know what might have gone wrong that it has not produced pullf.xvg 
and pullx.xvg files.



Kind regards,
chetan.



Forschungszentrum Juelich GmbH
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Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt


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Re: Antw: [gmx-users] NaN error using mdrun-gpu

[Szilárd Páll]

Hi,

Tesla C1060 and S1070 should is definitely supported so it's strange
that you get that warning. The only thing I can think of is that for
some reason the CUDA runtime reports the name of the GPUS other than
C1060/S1070. Could you please run the deviceQuery from the SDK and
provide the output here?

However, that should not be causing the NaN issue. Does the same
simulation run on the CPU?

Cheers,
--
Szilárd



2010/12/15 Bongkeun Kim :
> Hello,
>
> I tried using 1fs timestep and it did not work.
> I'm using nvidia T10 gpus(c1060 or s1070) and mdrun-gpu said it's not
> supported gpu and I had to use "force-device=y". Do you think this is the
> reason of the error?
> Thanks.
> Bongkeun Kim
>
> Quoting Emanuel Peter :
>
>> Hello,
>>
>> If you use for your timestep 1fs instead of 2fs, it could run better.
>>
>> Bests,
>>
>> Emanuel
>>
> Bongkeun Kim  15.12.10 8.36 Uhr >>>
>>
>> Hello,
>>
>>
>>
>> I got an error log when I used gromacs-gpu on npt simulation.
>>
>> The error is like:
>>
>> ---
>>
>> Input Parameters:
>>
>>    integrator           = md
>>
>>    nsteps               = 5000
>>
>>    init_step            = 0
>>
>>    ns_type              = Grid
>>
>>    nstlist              = 5
>>
>>    ndelta               = 2
>>
>>    nstcomm              = 10
>>
>>    comm_mode            = Linear
>>
>>    nstlog               = 1000
>>
>>    nstxout              = 1000
>>
>>    nstvout              = 1000
>>
>>    nstfout              = 0
>>
>>    nstcalcenergy        = 5
>>
>>    nstenergy            = 1000
>>
>>    nstxtcout            = 1000
>>
>>    init_t               = 0
>>
>>    delta_t              = 0.002
>>
>>    xtcprec              = 1000
>>
>>    nkx                  = 32
>>
>>    nky                  = 32
>>
>>    nkz                  = 32
>>
>>    pme_order            = 4
>>
>>    ewald_rtol           = 1e-05
>>
>>    ewald_geometry       = 0
>>
>>    epsilon_surface      = 0
>>
>>    optimize_fft         = FALSE
>>
>>    ePBC                 = xyz
>>
>>    bPeriodicMols        = FALSE
>>
>>    bContinuation        = TRUE
>>
>>    bShakeSOR            = FALSE
>>
>>    etc                  = V-rescale
>>
>>    nsttcouple           = 5
>>
>>    epc                  = Parrinello-Rahman
>>
>>    epctype              = Isotropic
>>
>>    nstpcouple           = 5
>>
>>    tau_p                = 2
>>
>>    ref_p (3x3):
>>
>>       ref_p[    0]={ 1.0e+00,  0.0e+00,  0.0e+00}
>>
>>       ref_p[    1]={ 0.0e+00,  1.0e+00,  0.0e+00}
>>
>>       ref_p[    2]={ 0.0e+00,  0.0e+00,  1.0e+00}
>>
>>    compress (3x3):
>>
>>       compress[    0]={ 4.5e-05,  0.0e+00,  0.0e+00}
>>
>>       compress[    1]={ 0.0e+00,  4.5e-05,  0.0e+00}
>>
>>       compress[    2]={ 0.0e+00,  0.0e+00,  4.5e-05}
>>
>>    refcoord_scaling     = No
>>
>>    posres_com (3):
>>
>>       posres_com[0]= 0.0e+00
>>
>>       posres_com[1]= 0.0e+00
>>
>>       posres_com[2]= 0.0e+00
>>
>>    posres_comB (3):
>>
>>       posres_comB[0]= 0.0e+00
>>
>>       posres_comB[1]= 0.0e+00
>>
>>       posres_comB[2]= 0.0e+00
>>
>>    andersen_seed        = 815131
>>
>>    rlist                = 1
>>
>>    rlistlong            = 1
>>
>>    rtpi                 = 0.05
>>
>>    coulombtype          = PME
>>
>>    rcoulomb_switch      = 0
>>
>>    rcoulomb             = 1
>>
>>    vdwtype              = Cut-off
>>
>>    rvdw_switch          = 0
>>
>>    rvdw                 = 1
>>
>>    epsilon_r            = 1
>>
>>    epsilon_rf           = 1
>>
>>    tabext               = 1
>>
>>    implicit_solvent     = No
>>
>>    gb_algorithm         = Still
>>
>>    gb_epsilon_solvent   = 80
>>
>>    nstgbradii           = 1
>>
>>    rgbradii             = 1
>>
>>    gb_saltconc          = 0
>>
>>    gb_obc_alpha         = 1
>>
>>    gb_obc_beta          = 0.8
>>
>>    gb_obc_gamma         = 4.85
>>
>>    gb_dielectric_offset = 0.009
>>
>>    sa_algorithm         = Ace-approximation
>>
>>    sa_surface_tension   = 2.05016
>>
>>    DispCorr             = EnerPres
>>
>>    free_energy          = no
>>
>>    init_lambda          = 0
>>
>>    delta_lambda         = 0
>>
>>    n_foreign_lambda     = 0
>>
>>    sc_alpha             = 0
>>
>>    sc_power             = 0
>>
>>    sc_sigma             = 0.3
>>
>>    sc_sigma_min         = 0.3
>>
>>    nstdhdl              = 10
>>
>>    separate_dhdl_file   = yes
>>
>>    dhdl_derivatives     = yes
>>
>>    dh_hist_size         = 0
>>
>>    dh_hist_spacing      = 0.1
>>
>>    nwall                = 0
>>
>>    wall_type            = 9-3
>>
>>    wall_atomtype[0]     = -1
>>
>>    wall_atomtype[1]     = -1
>>
>>    wall_density[0]      = 0
>>
>>    wall_density[1]      = 0
>>
>>    wall_ewald_zfac      = 3
>>
>>    pull                 = no
>>
>>    disre                = No
>>
>>    disre_weighting      = Conservative
>>
>>    disre_mixed          = FALSE
>>

[gmx-users] g_rotacf NH vector relaxation

[Olga Ivchenko]

Dear gromacs users,

I want to calculate NH vector for my ligand simulations using g_rotacf. I
want to ask if I first need to remove rotation and translation degrees of
freedom from the trajectory using the command:
trjconv -f traj.xtc -s 10nsProd_MD.tpr -fit rot+trans -o no_rot_trans.xtc

Also, when I am using this command which group I should select for least
square fit (ligand or the whole system) and a group for output.

The rotation correlation functions  (g_rotacf) output depends on trajectory
type which I have. So C(t) graphics are different if I remove rotation and
translation degrees of freedom.

Please can you advice me on this?




Yours sincerely,
Olga
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[gmx-users] Question about Extention simulation in REMD

[Qin Qiao]

Dear Sir or Madam,

I wonder how to continue a REMD running using .cpt file in Gromacs 4.5.1.
Since I ran a REMD of 56 replicas, there are one cpt file for each replica..
I couldn't do it by

tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
mdrun -s next.tpr -cpi previous.cpt


I guess it's not for an iterative line in the answer in
http://www.mail-archive.com/gmx-users@gromacs.org/msg33566.html, since the
mdrun should run simultaneously.

Could you give some advice? Thanks.

Best,

Qin
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Antw: Re: Antw: [gmx-users] NaN error using mdrun-gpu

[Emanuel Peter]

Hello

Did you use constraints = none instead of LINCS.
It could work better

bests,

Emanuel

>>> Bongkeun Kim  15.12.10 9.42 Uhr >>>
Hello,



I tried using 1fs timestep and it did not work.

I'm using nvidia T10 gpus(c1060 or s1070) and mdrun-gpu said it's not  

supported gpu and I had to use "force-device=y". Do you think this is  

the reason of the error?

Thanks.

Bongkeun Kim



Quoting Emanuel Peter :



> Hello,

>

> If you use for your timestep 1fs instead of 2fs, it could run better.

>

> Bests,

>

> Emanuel

>

 Bongkeun Kim  15.12.10 8.36 Uhr >>>

> Hello,

>

>

>

> I got an error log when I used gromacs-gpu on npt simulation.

>

> The error is like:

>

> ---

>

> Input Parameters:

>

> integrator   = md

>

> nsteps   = 5000

>

> init_step= 0

>

> ns_type  = Grid

>

> nstlist  = 5

>

> ndelta   = 2

>

> nstcomm  = 10

>

> comm_mode= Linear

>

> nstlog   = 1000

>

> nstxout  = 1000

>

> nstvout  = 1000

>

> nstfout  = 0

>

> nstcalcenergy= 5

>

> nstenergy= 1000

>

> nstxtcout= 1000

>

> init_t   = 0

>

> delta_t  = 0.002

>

> xtcprec  = 1000

>

> nkx  = 32

>

> nky  = 32

>

> nkz  = 32

>

> pme_order= 4

>

> ewald_rtol   = 1e-05

>

> ewald_geometry   = 0

>

> epsilon_surface  = 0

>

> optimize_fft = FALSE

>

> ePBC = xyz

>

> bPeriodicMols= FALSE

>

> bContinuation= TRUE

>

> bShakeSOR= FALSE

>

> etc  = V-rescale

>

> nsttcouple   = 5

>

> epc  = Parrinello-Rahman

>

> epctype  = Isotropic

>

> nstpcouple   = 5

>

> tau_p= 2

>

> ref_p (3x3):

>

>ref_p[0]={ 1.0e+00,  0.0e+00,  0.0e+00}

>

>ref_p[1]={ 0.0e+00,  1.0e+00,  0.0e+00}

>

>ref_p[2]={ 0.0e+00,  0.0e+00,  1.0e+00}

>

> compress (3x3):

>

>compress[0]={ 4.5e-05,  0.0e+00,  0.0e+00}

>

>compress[1]={ 0.0e+00,  4.5e-05,  0.0e+00}

>

>compress[2]={ 0.0e+00,  0.0e+00,  4.5e-05}

>

> refcoord_scaling = No

>

> posres_com (3):

>

>posres_com[0]= 0.0e+00

>

>posres_com[1]= 0.0e+00

>

>posres_com[2]= 0.0e+00

>

> posres_comB (3):

>

>posres_comB[0]= 0.0e+00

>

>posres_comB[1]= 0.0e+00

>

>posres_comB[2]= 0.0e+00

>

> andersen_seed= 815131

>

> rlist= 1

>

> rlistlong= 1

>

> rtpi = 0.05

>

> coulombtype  = PME

>

> rcoulomb_switch  = 0

>

> rcoulomb = 1

>

> vdwtype  = Cut-off

>

> rvdw_switch  = 0

>

> rvdw = 1

>

> epsilon_r= 1

>

> epsilon_rf   = 1

>

> tabext   = 1

>

> implicit_solvent = No

>

> gb_algorithm = Still

>

> gb_epsilon_solvent   = 80

>

> nstgbradii   = 1

>

> rgbradii = 1

>

> gb_saltconc  = 0

>

> gb_obc_alpha = 1

>

> gb_obc_beta  = 0.8

>

> gb_obc_gamma = 4.85

>

> gb_dielectric_offset = 0.009

>

> sa_algorithm = Ace-approximation

>

> sa_surface_tension   = 2.05016

>

> DispCorr = EnerPres

>

> free_energy  = no

>

> init_lambda  = 0

>

> delta_lambda = 0

>

> n_foreign_lambda = 0

>

> sc_alpha = 0

>

> sc_power = 0

>

> sc_sigma = 0.3

>

> sc_sigma_min = 0.3

>

> nstdhdl  = 10

>

> separate_dhdl_file   = yes

>

> dhdl_derivatives = yes

>

> dh_hist_size = 0

>

> dh_hist_spacing  = 0.1

>

> nwall= 0

>

> wall_type= 9-3

>

> wall_atomtype[0] = -1

>

> wall_atomtype[1] = -1

>

> wall_density[0]  = 0

>

> wall_density[1]  = 0

>

> wall_ewald_zfac  = 3

>

> pull = no

>

> disre= No

>

> disre_weighting  = Conservative

>

> disre_mixed  = FALSE

>

> dr_fc= 1000

>

> dr_tau   = 0

>

> nstdisreout  = 100

>

> orires_fc= 0

>

> orires_tau   = 0

>

> nstorireout  = 100

>

RE: [gmx-users] pathologically expanding box

[Berk Hess]

Hi,

I think the problem is epsilon_r=80, which reduces your electrostatics 
interactions
by a factor of 80.

Berk

> Date: Mon, 13 Dec 2010 17:46:14 -0500
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] pathologically expanding box
> 
> 
> 
> Greg Bowman wrote:
> > Hello,
> > 
> > Has anyone else experienced a pathologically expanding box during 
> > equilibration in the NPT ensemble?  I've solvated my system with 
> > editconf/genbox, energy minimized, equilibrated in NVT with the protein 
> > coordinates restrained, and then equilibrated in NPT without any 
> > position restraints.  During the NPT equilibration all the box 
> > dimensions are doubling and the density decreases drastically.
> > 
> > I'm using the v-rescale thermostat and the Berendsen barostat in gromacs 
> > 4.5.3 with the AMBER03 force field and tip3p water.  I've also tried 
> > OPLSAA with SPC water, a number of different box types (cubic, 
> > octahedral, dodecahedral), and shorter tau_t and tau_p settings.  I also 
> > tried adding another energy minimzation step between my NVT and NPT phases.
> > 
> 
> Is the temperature, potential energy, etc. stable after NVT?
> 
> Is the increase in box size steady, oscillating, or sudden?
> 
> Does the problem persist with different combinations of thermostat and 
> barostat, 
> or is it limited to V-rescale + Berendsen?
> 
> -Justin
> 
> > My mdp settings for the NPT ensemble are below.
> > 
> > Thanks for your help.
> > 
> > Greg
> > 
> > ; RUN CONTROL PARAMETERS
> > ;define  = -DPOSRES
> > integrator  = md
> > tinit   = 0
> > nsteps  = 5
> > dt  = 0.002000
> > comm-mode   = linear
> > nstcomm = 4
> > 
> > ; CONSTRAINTS
> > constraints = all-bonds
> > lincs_order = 6
> > lincs_iter  = 2
> > 
> > ; NEIGHBORSEARCHING PARAMETERS
> > ns_type = grid
> > nstlist = 4
> > rlist   = 1.2
> > pbc = xyz
> > 
> > ; ELECTROSTATICS
> > coulombtype = pme ;-switch
> > rcoulomb= 1.2
> > ;rcoulomb-switch = 0.80
> > fourierspacing  = 0.12
> > fourier_nx  = 0
> > fourier_ny  = 0
> > fourier_nz  = 0
> > pme_order   = 6
> > ewald_rtol  = 0.01
> > ewald_geometry  = 3d
> > epsilon_surface = 0
> > optimize_fft= yes
> > epsilon_r   = 80
> > 
> > ; VDW
> > vdw-type= switch
> > rvdw= 1.2
> > rvdw-switch = 1.1
> > DispCorr= EnerPres
> > 
> > ; OUTPUT CONTROL OPTIONS
> > ; Output frequency for coords (x), velocities (v) and forces (f) =
> > nstxout = 0
> > nstvout = 0
> > nstfout = 0
> > nstlog  = 0
> > energygrps  = System
> > nstenergy   = 100
> > nstcalcenergy   = 1
> > nstxtcout   = 0
> > xtc-grps= Protein
> > 
> > Tcoupl  = v-rescale
> > tau_t   = 0.5
> > tc-grps = System
> > ref_t   = 300
> > ld_seed = -1
> > 
> > Pcoupl  = berendsen
> > Pcoupltype  = isotropic
> > tau_p   = 5
> > compressibility = 4.5e-5
> > ref_p   = 1.0
> > 
> > gen_vel = yes
> > gen_temp= 300.0
> > gen_seed= -1
> > 
> > 
> 
> -- 
> 
> 
> 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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Re: Antw: [gmx-users] NaN error using mdrun-gpu

[Bongkeun Kim]

Hello,

I tried using 1fs timestep and it did not work.
I'm using nvidia T10 gpus(c1060 or s1070) and mdrun-gpu said it's not  
supported gpu and I had to use "force-device=y". Do you think this is  
the reason of the error?

Thanks.
Bongkeun Kim

Quoting Emanuel Peter :


Hello,

If you use for your timestep 1fs instead of 2fs, it could run better.

Bests,

Emanuel


Bongkeun Kim  15.12.10 8.36 Uhr >>>

Hello,



I got an error log when I used gromacs-gpu on npt simulation.

The error is like:

---

Input Parameters:

integrator   = md

nsteps   = 5000

init_step= 0

ns_type  = Grid

nstlist  = 5

ndelta   = 2

nstcomm  = 10

comm_mode= Linear

nstlog   = 1000

nstxout  = 1000

nstvout  = 1000

nstfout  = 0

nstcalcenergy= 5

nstenergy= 1000

nstxtcout= 1000

init_t   = 0

delta_t  = 0.002

xtcprec  = 1000

nkx  = 32

nky  = 32

nkz  = 32

pme_order= 4

ewald_rtol   = 1e-05

ewald_geometry   = 0

epsilon_surface  = 0

optimize_fft = FALSE

ePBC = xyz

bPeriodicMols= FALSE

bContinuation= TRUE

bShakeSOR= FALSE

etc  = V-rescale

nsttcouple   = 5

epc  = Parrinello-Rahman

epctype  = Isotropic

nstpcouple   = 5

tau_p= 2

ref_p (3x3):

   ref_p[0]={ 1.0e+00,  0.0e+00,  0.0e+00}

   ref_p[1]={ 0.0e+00,  1.0e+00,  0.0e+00}

   ref_p[2]={ 0.0e+00,  0.0e+00,  1.0e+00}

compress (3x3):

   compress[0]={ 4.5e-05,  0.0e+00,  0.0e+00}

   compress[1]={ 0.0e+00,  4.5e-05,  0.0e+00}

   compress[2]={ 0.0e+00,  0.0e+00,  4.5e-05}

refcoord_scaling = No

posres_com (3):

   posres_com[0]= 0.0e+00

   posres_com[1]= 0.0e+00

   posres_com[2]= 0.0e+00

posres_comB (3):

   posres_comB[0]= 0.0e+00

   posres_comB[1]= 0.0e+00

   posres_comB[2]= 0.0e+00

andersen_seed= 815131

rlist= 1

rlistlong= 1

rtpi = 0.05

coulombtype  = PME

rcoulomb_switch  = 0

rcoulomb = 1

vdwtype  = Cut-off

rvdw_switch  = 0

rvdw = 1

epsilon_r= 1

epsilon_rf   = 1

tabext   = 1

implicit_solvent = No

gb_algorithm = Still

gb_epsilon_solvent   = 80

nstgbradii   = 1

rgbradii = 1

gb_saltconc  = 0

gb_obc_alpha = 1

gb_obc_beta  = 0.8

gb_obc_gamma = 4.85

gb_dielectric_offset = 0.009

sa_algorithm = Ace-approximation

sa_surface_tension   = 2.05016

DispCorr = EnerPres

free_energy  = no

init_lambda  = 0

delta_lambda = 0

n_foreign_lambda = 0

sc_alpha = 0

sc_power = 0

sc_sigma = 0.3

sc_sigma_min = 0.3

nstdhdl  = 10

separate_dhdl_file   = yes

dhdl_derivatives = yes

dh_hist_size = 0

dh_hist_spacing  = 0.1

nwall= 0

wall_type= 9-3

wall_atomtype[0] = -1

wall_atomtype[1] = -1

wall_density[0]  = 0

wall_density[1]  = 0

wall_ewald_zfac  = 3

pull = no

disre= No

disre_weighting  = Conservative

disre_mixed  = FALSE

dr_fc= 1000

dr_tau   = 0

nstdisreout  = 100

orires_fc= 0

orires_tau   = 0

nstorireout  = 100

dihre-fc = 1000

em_stepsize  = 0.01

em_tol   = 10

niter= 20

fc_stepsize  = 0

nstcgsteep   = 1000

nbfgscorr= 10

ConstAlg = Lincs

shake_tol= 0.0001

lincs_order  = 4

lincs_warnangle  = 30

lincs_iter   = 1

bd_fric  = 0

ld_seed  = 1993

cos_accel= 0

deform (3x3):

   deform[0]={ 0.0e+00,  0.0e+00,  0.0e+00}

   deform[1]={ 0.0e+00,  0.0e+00,  0.0e+00}

   deform[2]={ 0.0e+00,  0.0e+00,  0.0e+00}

userint1 = 0

userint2

Antw: [gmx-users] NaN error using mdrun-gpu

[Emanuel Peter]

Hello,

If you use for your timestep 1fs instead of 2fs, it could run better.

Bests,

Emanuel  

>>> Bongkeun Kim  15.12.10 8.36 Uhr >>>
Hello,



I got an error log when I used gromacs-gpu on npt simulation.

The error is like:

---

Input Parameters:

integrator   = md

nsteps   = 5000

init_step= 0

ns_type  = Grid

nstlist  = 5

ndelta   = 2

nstcomm  = 10

comm_mode= Linear

nstlog   = 1000

nstxout  = 1000

nstvout  = 1000

nstfout  = 0

nstcalcenergy= 5

nstenergy= 1000

nstxtcout= 1000

init_t   = 0

delta_t  = 0.002

xtcprec  = 1000

nkx  = 32

nky  = 32

nkz  = 32

pme_order= 4

ewald_rtol   = 1e-05

ewald_geometry   = 0

epsilon_surface  = 0

optimize_fft = FALSE

ePBC = xyz

bPeriodicMols= FALSE

bContinuation= TRUE

bShakeSOR= FALSE

etc  = V-rescale

nsttcouple   = 5

epc  = Parrinello-Rahman

epctype  = Isotropic

nstpcouple   = 5

tau_p= 2

ref_p (3x3):

   ref_p[0]={ 1.0e+00,  0.0e+00,  0.0e+00}

   ref_p[1]={ 0.0e+00,  1.0e+00,  0.0e+00}

   ref_p[2]={ 0.0e+00,  0.0e+00,  1.0e+00}

compress (3x3):

   compress[0]={ 4.5e-05,  0.0e+00,  0.0e+00}

   compress[1]={ 0.0e+00,  4.5e-05,  0.0e+00}

   compress[2]={ 0.0e+00,  0.0e+00,  4.5e-05}

refcoord_scaling = No

posres_com (3):

   posres_com[0]= 0.0e+00

   posres_com[1]= 0.0e+00

   posres_com[2]= 0.0e+00

posres_comB (3):

   posres_comB[0]= 0.0e+00

   posres_comB[1]= 0.0e+00

   posres_comB[2]= 0.0e+00

andersen_seed= 815131

rlist= 1

rlistlong= 1

rtpi = 0.05

coulombtype  = PME

rcoulomb_switch  = 0

rcoulomb = 1

vdwtype  = Cut-off

rvdw_switch  = 0

rvdw = 1

epsilon_r= 1

epsilon_rf   = 1

tabext   = 1

implicit_solvent = No

gb_algorithm = Still

gb_epsilon_solvent   = 80

nstgbradii   = 1

rgbradii = 1

gb_saltconc  = 0

gb_obc_alpha = 1

gb_obc_beta  = 0.8

gb_obc_gamma = 4.85

gb_dielectric_offset = 0.009

sa_algorithm = Ace-approximation

sa_surface_tension   = 2.05016

DispCorr = EnerPres

free_energy  = no

init_lambda  = 0

delta_lambda = 0

n_foreign_lambda = 0

sc_alpha = 0

sc_power = 0

sc_sigma = 0.3

sc_sigma_min = 0.3

nstdhdl  = 10

separate_dhdl_file   = yes

dhdl_derivatives = yes

dh_hist_size = 0

dh_hist_spacing  = 0.1

nwall= 0

wall_type= 9-3

wall_atomtype[0] = -1

wall_atomtype[1] = -1

wall_density[0]  = 0

wall_density[1]  = 0

wall_ewald_zfac  = 3

pull = no

disre= No

disre_weighting  = Conservative

disre_mixed  = FALSE

dr_fc= 1000

dr_tau   = 0

nstdisreout  = 100

orires_fc= 0

orires_tau   = 0

nstorireout  = 100

dihre-fc = 1000

em_stepsize  = 0.01

em_tol   = 10

niter= 20

fc_stepsize  = 0

nstcgsteep   = 1000

nbfgscorr= 10

ConstAlg = Lincs

shake_tol= 0.0001

lincs_order  = 4

lincs_warnangle  = 30

lincs_iter   = 1

bd_fric  = 0

ld_seed  = 1993

cos_accel= 0

deform (3x3):

   deform[0]={ 0.0e+00,  0.0e+00,  0.0e+00}

   deform[1]={ 0.0e+00,  0.0e+00,  0.0e+00}

   deform[2]={ 0.0e+00,  0.0e+00,  0.0e+00}

userint1 = 0

userint2 = 0

userint3 = 0

userint4 = 0

userreal1= 0

userreal2= 0

userreal3= 0

userreal4= 0

grpopts:

nrdf:   24715

ref_t: 325

tau_t: 0.1