Re: [gmx-users] System blowing up in Gromacsv5.0.5 but not in v4.5.4

[Justin Lemkul]

On 12/16/15 12:54 PM, NISHA Prakash wrote:

Dear Justin,

You are right and I totally agree with you. But, the point that I was
trying to make was that "the same input coordinates and input .mdp files
run in 4.5.4 and fail in 5.0.5".  Also, if this situation persists, does
that mean the results that have been obtained from the version 4.5.4 are
not reliable?

The second query was that - the topology and co-ordinates should be fine
because I have obtained these files from the simulation of protein alone in
version-5.0.5. Yet, I get LINCS warning for the protein atoms alone when I
simulate it as a complex with the ligand.
Kindly help me identify the problem.



You would have to actually do debugging on the code level to find out which 
function is failing, or at least follow 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System. 
 Simply saying the system fails provides exactly zero useful diagnostic 
information.


-Justin


Thanking you,
Nisha

On Wed, Dec 16, 2015 at 7:05 PM, Justin Lemkul  wrote:




On 12/16/15 12:08 AM, NISHA Prakash wrote:


Dear Justin,

I am simulating a protein ligand complex. The protein co-ordinate file
that
I have taken is an output of the simulation of the protein alone in
Gromacs-v5.0.5. The topology and the co-ordinates are fine. I am still
facing this problem wherein I get the LINCS warning for only the protein
atoms. The ligand also is fine.



If the protein fails, you have a problem somewhere.  That's either
topology (unlikely), coordinates (probable), or .mdp (most probable).  You
said in your earlier message that energy minimization failed, which points
to coordinates being the problem.

Like I mentioned before, I do not have this problem when I use the

Gromacs-4.5.4 where I have used the same co-ordinate file with different
ligands and same parameter file.



If you're comparing a protein-ligand complex in 5.0.5 against different
complexes in 4.5.4, that is a meaningless comparison.  It's apples and
oranges.  If the same input coordinates and input .mdp files run in 4.5.4
and fail in 5.0.5, that might be something to look into.  But the general
advice applies here - either way you're using outdated software, so if
something is failing, upgrade to the latest version and try again.

-Justin


Kindly let me know how to resolve the issue.


Thanking you in anticipation.

Nisha




On Wed, Dec 16, 2015 at 12:26 AM, Justin Lemkul  wrote:




On 12/15/15 8:42 AM, NISHA Prakash wrote:

Hi all,


I am trying to simulate a protein using similar parameters as in the
tutorial - Protein ligand by Justin Lemkul.

I am facing a problem wherein the protein simulation is exploding only
in
this version - Gromacs-v5.0.5 but not in the older version
Gromacs-v4.5.4.

The warning message is as follows

---
There were 4 inconsistent shifts. Check your topology

Steepest Descents:
  Tolerance (Fmax)   =  1.0e+03
  Number of steps=5

WARNING: Listed nonbonded interaction between particles 1312 and 1315
at distance 4.728 which is larger than the table limit 2.000 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the
table-extension
distance in the mdp file if you are really sure that is the reason.

ATOM   1312  O   TYR A 207
ATOM   1315  CD1 TYR A 207
-



---
em_real.mdp file

; LINES STARTING WITH ';' ARE COMMENTS
title = Minimization ; Title of run

; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0   ; Stop minimization when the maximum force < 10.0
kJ/mol
emstep  = 0.01  ; Energy step size
nsteps = 5   ; Maximum number of (minimization) steps to perform
energygrps = Protein ; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how
to
calculate the interactions
nstlist= 1; Frequency to update the neighbor list and long range
forces
cutoff-scheme   = Verlet
ns_type= grid ; Method to determine neighbor list (simple, grid)
rlist= 1.0 ; Cut-off for making neighbor list (short range forces)
coulombtype= PME ; Treatment of long range electrostatic
interactions
rcoulomb= 1.0 ; long range electrostatic cut-off
rvdw= 1.0 ; long range Van der Waals 

Re: [gmx-users] Help with editconf

[Tsjerk Wassenaar]

Hi Rita,

You'll need to make/use an index file (gmx make_ndx).

Cheers,

Tsjerk

On Wed, Dec 16, 2015 at 7:06 PM, Rita Melo  wrote:

> Dear all,
>
> I'm using editconf and I need to select several groups at same time. How to
> do that?
>
> Thanks!
> Rita.
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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>



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[gmx-users] periodic improper dihedral

[Eric Smoll]

Hello GROMACS users,

I have a question about specifying periodic improper dihedrals in GROMACS.

In the GROMACS manual (chapter 5, table 5.5), the parameters of the
periodic improper dihedral are listed as follows:

phi_s ( deg ); k_phi (kJ mol^-1); multiplicity

In the GROMACS manual (chapter 4, equation 4.60), the form of the periodic
improper dihedral is specified as

V_d( phi_ijkl ) = k_phi ( 1 - cos(n*phi - phi_s))

Am I correct in assuming that "n" shown is the "multiplicity" listed above?

Best,
Eric
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[gmx-users] Short how-to for installing GROMACS with CUDA ...

[Téletchéa Stéphane]

Dear all,

I have struggled recently in getting gromacs-aware of cuda capabilities.
After searching for a "while" (one afternoon), I removed the ubuntu-provided
drivers and packages (which worked in the past) and installed everything
"from scratch". It seems this is both coming from NVIDIA requiring the
"GPU deployment kit" in addition to the cuda toolkit, and from GROMACS
only warning about the missing NVML (but not failing while asking for 
GPU compilation).


In short, I have put the executive commands there:
http://www.steletch.org/spip.php?article89

As some messages on the list are about this "problem", I thought it 
would be

helpful to all.

Best,

Stéphane

--
Assistant Professor, UFIP, UMR 6286 CNRS, Team Protein Design In Silico
UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes 
cedex 03, France
Tél : +33 251 125 636 / Fax : +33 251 125 632
http://www.ufip.univ-nantes.fr/ - http://www.steletch.org

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Re: [gmx-users] System blowing up in Gromacsv5.0.5 but not in v4.5.4

[NISHA Prakash]

Dear Justin,

You are right and I totally agree with you. But, the point that I was
trying to make was that "the same input coordinates and input .mdp files
run in 4.5.4 and fail in 5.0.5".  Also, if this situation persists, does
that mean the results that have been obtained from the version 4.5.4 are
not reliable?

The second query was that - the topology and co-ordinates should be fine
because I have obtained these files from the simulation of protein alone in
version-5.0.5. Yet, I get LINCS warning for the protein atoms alone when I
simulate it as a complex with the ligand.
Kindly help me identify the problem.

Thanking you,
Nisha

On Wed, Dec 16, 2015 at 7:05 PM, Justin Lemkul  wrote:

>
>
> On 12/16/15 12:08 AM, NISHA Prakash wrote:
>
>> Dear Justin,
>>
>> I am simulating a protein ligand complex. The protein co-ordinate file
>> that
>> I have taken is an output of the simulation of the protein alone in
>> Gromacs-v5.0.5. The topology and the co-ordinates are fine. I am still
>> facing this problem wherein I get the LINCS warning for only the protein
>> atoms. The ligand also is fine.
>>
>
> If the protein fails, you have a problem somewhere.  That's either
> topology (unlikely), coordinates (probable), or .mdp (most probable).  You
> said in your earlier message that energy minimization failed, which points
> to coordinates being the problem.
>
> Like I mentioned before, I do not have this problem when I use the
>> Gromacs-4.5.4 where I have used the same co-ordinate file with different
>> ligands and same parameter file.
>>
>>
> If you're comparing a protein-ligand complex in 5.0.5 against different
> complexes in 4.5.4, that is a meaningless comparison.  It's apples and
> oranges.  If the same input coordinates and input .mdp files run in 4.5.4
> and fail in 5.0.5, that might be something to look into.  But the general
> advice applies here - either way you're using outdated software, so if
> something is failing, upgrade to the latest version and try again.
>
> -Justin
>
>
> Kindly let me know how to resolve the issue.
>>
>> Thanking you in anticipation.
>>
>> Nisha
>>
>>
>>
>>
>> On Wed, Dec 16, 2015 at 12:26 AM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 12/15/15 8:42 AM, NISHA Prakash wrote:
>>>
>>> Hi all,

 I am trying to simulate a protein using similar parameters as in the
 tutorial - Protein ligand by Justin Lemkul.

 I am facing a problem wherein the protein simulation is exploding only
 in
 this version - Gromacs-v5.0.5 but not in the older version
 Gromacs-v4.5.4.

 The warning message is as follows

 ---
 There were 4 inconsistent shifts. Check your topology

 Steepest Descents:
  Tolerance (Fmax)   =  1.0e+03
  Number of steps=5

 WARNING: Listed nonbonded interaction between particles 1312 and 1315
 at distance 4.728 which is larger than the table limit 2.000 nm.

 This is likely either a 1,4 interaction, or a listed interaction inside
 a smaller molecule you are decoupling during a free energy calculation.
 Since interactions at distances beyond the table cannot be computed,
 they are skipped until they are inside the table limit again. You will
 only see this message once, even if it occurs for several interactions.

 IMPORTANT: This should not happen in a stable simulation, so there is
 probably something wrong with your system. Only change the
 table-extension
 distance in the mdp file if you are really sure that is the reason.
 
 ATOM   1312  O   TYR A 207
 ATOM   1315  CD1 TYR A 207
 -



 ---
 em_real.mdp file

 ; LINES STARTING WITH ';' ARE COMMENTS
 title = Minimization ; Title of run

 ; Parameters describing what to do, when to stop and what to save
 integrator = steep ; Algorithm (steep = steepest descent minimization)
 emtol = 1000.0   ; Stop minimization when the maximum force < 10.0
 kJ/mol
 emstep  = 0.01  ; Energy step size
 nsteps = 5   ; Maximum number of (minimization) steps to perform
 energygrps = Protein ; Which energy group(s) to write to disk

 ; Parameters describing how to find the neighbors of each atom and how
 to
 calculate the interactions
 nstlist= 1; Frequency to update the neighbor list and long range
 forces
 cutoff-scheme   = Verlet
 ns_type= grid ; Method to determine neighbor list (simple, grid)
 rlist= 1.0 ; Cut-off for making neighbor list (short range forces)
 coulombtype= PME ; Treatment of long range electrostatic
 interactions
 rcoulomb= 1.0 ; long range electrostatic cut-off

[gmx-users] PBSA calculations

[Mishelle Oña]

HiI have a question about calculation of solvation energy using PBSA. From this 
approach the G solvation is the sum of the G polar + G nonpolar energy, if I am 
calculating the solvation of a nonpolar molecule in water I want to know if iin 
this case G polar is  0? Samara   
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[gmx-users] Problems with energy minimization

[ibrahim khalil]

Dear GROMACS users,

I am simulating a curved carbon nanotubes in GROMACS. When I do the energy
minimization to the structure, I am getting different types of structures
depending on the value of 'emtol'.

For instance, if the emtol value is very small (below 100) the structure
has a lot of roughness and if the emtol is large (greater than 1000) the
structure is more or less the same to the initial structure.
If I am having an emtol of about 300, the roughness is minimized (yet, it
is present)

My question is, how can i decide which value of emtol is to be used?

Any thought on this or any help would be highly appreciated.

Thanks in advance
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[gmx-users] Help with editconf

[Rita Melo]

Dear all,

I'm using editconf and I need to select several groups at same time. How to
do that?

Thanks!
Rita.

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Re: [gmx-users] PBSA calculations

[Justin Lemkul]

On 12/16/15 1:04 PM, Mishelle Oña wrote:

HiI have a question about calculation of solvation energy using PBSA. From this 
approach the G solvation is the sum of the G polar + G nonpolar energy, if I am 
calculating the solvation of a nonpolar molecule in water I want to know if iin 
this case G polar is  0? Samara 



Only if all the atoms have zero charge.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] PBSA calculations

[Justin Lemkul]

On 12/16/15 1:21 PM, Mishelle Oña wrote:

My polimer has total charge 0, you mean that?


No, I mean what I said. Gpolar = 0 if all of the *atoms* have zero charge. 
Anything with a charge has an electrostatic interaction with solvent (continuum 
or otherwise).  The net charge of a molecule is irrelevant in this context.


-Justin


Samara


To: gmx-us...@gromacs.org
From: jalem...@vt.edu
Date: Wed, 16 Dec 2015 13:18:48 -0500
Subject: Re: [gmx-users] PBSA calculations



On 12/16/15 1:04 PM, Mishelle Oña wrote:

HiI have a question about calculation of solvation energy using PBSA. From this 
approach the G solvation is the sum of the G polar + G nonpolar energy, if I am 
calculating the solvation of a nonpolar molecule in water I want to know if iin 
this case G polar is  0? Samara 



Only if all the atoms have zero charge.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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mail to gmx-users-requ...@gromacs.org.





--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] PBSA calculations

[Mishelle Oña]

My polimer has total charge 0, you mean that?
Samara

> To: gmx-us...@gromacs.org
> From: jalem...@vt.edu
> Date: Wed, 16 Dec 2015 13:18:48 -0500
> Subject: Re: [gmx-users] PBSA calculations
> 
> 
> 
> On 12/16/15 1:04 PM, Mishelle Oña wrote:
> > HiI have a question about calculation of solvation energy using PBSA. From 
> > this approach the G solvation is the sum of the G polar + G nonpolar 
> > energy, if I am calculating the solvation of a nonpolar molecule in water I 
> > want to know if iin this case G polar is  0? Samara 
> > 
> >
> 
> Only if all the atoms have zero charge.
> 
> -Justin
> 
> -- 
> ==
> 
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> 
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
> 
> ==
> -- 
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Re: [gmx-users] Problems with energy minimization

[Mark Abraham]

Hi,

The answer lies why you are doing em...

Mark

On Thu, 17 Dec 2015 04:43 ibrahim khalil 
wrote:

> Dear GROMACS users,
>
> I am simulating a curved carbon nanotubes in GROMACS. When I do the energy
> minimization to the structure, I am getting different types of structures
> depending on the value of 'emtol'.
>
> For instance, if the emtol value is very small (below 100) the structure
> has a lot of roughness and if the emtol is large (greater than 1000) the
> structure is more or less the same to the initial structure.
> If I am having an emtol of about 300, the roughness is minimized (yet, it
> is present)
>
> My question is, how can i decide which value of emtol is to be used?
>
> Any thought on this or any help would be highly appreciated.
>
> Thanks in advance
> --
> Gromacs Users mailing list
>
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> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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>
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Re: [gmx-users] periodic improper dihedral

[Mark Abraham]

Yes

On Thu, 17 Dec 2015 05:39 Eric Smoll  wrote:

> Hello GROMACS users,
>
> I have a question about specifying periodic improper dihedrals in GROMACS.
>
> In the GROMACS manual (chapter 5, table 5.5), the parameters of the
> periodic improper dihedral are listed as follows:
>
> phi_s ( deg ); k_phi (kJ mol^-1); multiplicity
>
> In the GROMACS manual (chapter 4, equation 4.60), the form of the periodic
> improper dihedral is specified as
>
> V_d( phi_ijkl ) = k_phi ( 1 - cos(n*phi - phi_s))
>
> Am I correct in assuming that "n" shown is the "multiplicity" listed above?
>
> Best,
> Eric
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[gmx-users] thermodynamic integration

[Sana Saeed]

how can we use Thermodynamic integration in gromacs for free energy 
analysis.any tutorial/script pleaseRegards Sana Saeed
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[gmx-users] POVPC MARTINI ff

[shivangi nangia]

Hello All,

I am looking for MARTINI ff for POVPC, its not on MARTNI webpage.

It will be great if anyone can help me with it.

Thanks in advance.

Regards,
sxn
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Re: [gmx-users] trajectory file

[Timofey Tyugashev]

16.12.2015 00:55, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет:
04.12.2015 14:43,gromacs.org_gmx-users-requ...@maillist.sys.kth.se  
>?:

>>I ran the production MD and got the trajectory file (xtcformat) but as
>>I?m new to MD I don?t know how to visualize it. I opened it withvmd
>>and it could read the atoms and frames but didn?t show anything when
>>playingthe frames. I don?t know whether another program can do it or
>>my xtc is notcorrect.

>You can also read GROMACS trajectories with PyMOL. It offers quite
>nice visualisation options.
>Use 'load' command to load the coordinate file first, then load the
>trajectory itself using 'load_traj' command.

Only problem with pymol is that it eats very large amount of memory. I
cannot evel load trajectory of large nucleoprotein complex (~200k atoms
for complex itself without solvent) if it has ~1000 frames on
workstation with 64G ram.
Personally  I haven't noticed any qualitative difference in memory 
consumption compared with vmd when viewing same .xtc files. It either 
works or it does not. But my simulations are different (~5-10k atoms 
without solvent and tens of ns on 32G RAM system).
IIRC, there were some options in pymol for processing trajectories. 
Maybe they do influence the performance.

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Re: [gmx-users] periodic improper dihedral

[Eric Smoll]

Thank you Mark,

We are having difficulty adding new parameters to the oplsaa forcefield in
"share/gromacs.top." We have a "[ dihedraltypes ]" directive where I add
fourier dihedral parameters (function type 5) and a "[ dihedraltypes ]"
directive where I add periodic improper dihedrals (function type 4). We
have itp/top files that contain two corresponding "[ dihedrals ]" directive.

Grompp is complaining that "No default proper/improper dihedral type."
Grompp also complains when the improper terms are represented with a proper
dihedral (function type 2).

Do you have any idea how I could trouble shoot this problem?

Best,
Eric

On Wed, Dec 16, 2015 at 4:54 PM, Mark Abraham 
wrote:

> Yes
>
> On Thu, 17 Dec 2015 05:39 Eric Smoll  wrote:
>
> > Hello GROMACS users,
> >
> > I have a question about specifying periodic improper dihedrals in
> GROMACS.
> >
> > In the GROMACS manual (chapter 5, table 5.5), the parameters of the
> > periodic improper dihedral are listed as follows:
> >
> > phi_s ( deg ); k_phi (kJ mol^-1); multiplicity
> >
> > In the GROMACS manual (chapter 4, equation 4.60), the form of the
> periodic
> > improper dihedral is specified as
> >
> > V_d( phi_ijkl ) = k_phi ( 1 - cos(n*phi - phi_s))
> >
> > Am I correct in assuming that "n" shown is the "multiplicity" listed
> above?
> >
> > Best,
> > Eric
> > --
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> > posting!
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> >
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[gmx-users] Fw: thermodynamic integration

[Sana Saeed]

 On Thursday, December 17, 2015 11:06 AM, Sana Saeed 
 wrote:
 

 how can we use Thermodynamic integration in gromacs for free energy 
analysis.any tutorial/script pleaseRegards Sana Saeed

  
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Re: [gmx-users] periodic improper dihedral

[Mark Abraham]

Hi,

Seeing the actual contents (e.g. via file sharing service) and error
message is usually better for finding the problem.

Mark

On Thu, 17 Dec 2015 12:29 Eric Smoll  wrote:

> Hello Mark,
>
> Thanks for the response. I am having trouble finding this "mismatch" and I
> want to make sure the overall procedure is correct. I outline a schematic
> below:
>
>  I add to the atomtypes file.
> opls_1000 12.011
> opls_1001 12.011
> etc...
>
>  In the oplsaa.ff directory, I add:
>
> [ atomtypes ]
> opls_1000  A_B  12  12.011  0.0  A  1.0e-01  1.0e-01
> opls_1001  C_D  12  12.011  0.0  A  1.0e-01  1.0e-01
> opls_1002  E_F  12  12.011  0.0  A  1.0e-01  1.0e-01
> opls_1003  G_H  12  12.011  0.0  A  1.0e-01  1.0e-01
> etc...
>
> [ bondtypes ]
> A_B  C_D  1  1.0  1.0
> etc...
>
> [ angletypes ]
> A_B  C_D  E_F  1  1.0  1.0
> etc...
>
> [ dihedraltypes ]
> A_B  C_D  E_F  G_H  5  1.0  1.0
> etc...
>
> [ dihedraltypes ]
> A_B  C_D  E_F  G_H  4  1.0  1.0
> etc...
>
>  Our CWD .itp files contain the following:
>
> [ moleculetype ]
> ; Name nrexcl
> TMP 3
>
> [ atoms ]
> ; nrtype  resn  residue atom  cgnr  charge  mass  typeB
> chargeB massB
> 1  opls_1001  1  TMP  C1  1  0.0 12.011
> 2  opls_1002  1  TMP  C2  2  0.0 12.011
> 3  opls_1003  1  TMP  C3  3  0.0 12.011
> 4  opls_1004  1  TMP  C4  4  0.0 12.011
> etc...
>
> [ bonds ]
> 1  2  1
> etc...
>
> [ angles ]
> 1  2  3  1
> etc...
>
> [ dihedrals ]
> 1  2  3  4  5
> etc...
>
> [ dihedrals ]
> 1  2  3  4  4
> etc...
>
>  The .top just includes the .itp's
>
> #include "oplsaa.ff/forcefield.itp"
> #include "TMP.itp"
>
> [ system ]
> TMP
>
> [ molecules ]
> TMP 1000
>
> ** Following this procedure, grompp delivers the error:
>
> ERROR 1 [file TMP.itp, line XXX]:
>   No default Improper Dih. types
>
> Is this workflow incorrect?
>
> Best,
> Eric
>
>
> On Wed, Dec 16, 2015 at 5:46 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > All that depends on is the atom types, so something there must not be
> > matching properly.
> >
> > Mark
> >
> > On Thu, 17 Dec 2015 10:15 Eric Smoll  wrote:
> >
> > > Thank you Mark,
> > >
> > > We are having difficulty adding new parameters to the oplsaa forcefield
> > in
> > > "share/gromacs.top." We have a "[ dihedraltypes ]" directive where I
> add
> > > fourier dihedral parameters (function type 5) and a "[ dihedraltypes ]"
> > > directive where I add periodic improper dihedrals (function type 4). We
> > > have itp/top files that contain two corresponding "[ dihedrals ]"
> > > directive.
> > >
> > > Grompp is complaining that "No default proper/improper dihedral type."
> > > Grompp also complains when the improper terms are represented with a
> > proper
> > > dihedral (function type 2).
> > >
> > > Do you have any idea how I could trouble shoot this problem?
> > >
> > > Best,
> > > Eric
> > >
> > > On Wed, Dec 16, 2015 at 4:54 PM, Mark Abraham <
> mark.j.abra...@gmail.com>
> > > wrote:
> > >
> > > > Yes
> > > >
> > > > On Thu, 17 Dec 2015 05:39 Eric Smoll  wrote:
> > > >
> > > > > Hello GROMACS users,
> > > > >
> > > > > I have a question about specifying periodic improper dihedrals in
> > > > GROMACS.
> > > > >
> > > > > In the GROMACS manual (chapter 5, table 5.5), the parameters of the
> > > > > periodic improper dihedral are listed as follows:
> > > > >
> > > > > phi_s ( deg ); k_phi (kJ mol^-1); multiplicity
> > > > >
> > > > > In the GROMACS manual (chapter 4, equation 4.60), the form of the
> > > > periodic
> > > > > improper dihedral is specified as
> > > > >
> > > > > V_d( phi_ijkl ) = k_phi ( 1 - cos(n*phi - phi_s))
> > > > >
> > > > > Am I correct in assuming that "n" shown is the "multiplicity"
> listed
> > > > above?
> > > > >
> > > > > Best,
> > > > > Eric
> > > > > --
> > > > > Gromacs Users mailing list
> > > > >
> > > > > * Please search the archive at
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> > > > > posting!
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Re: [gmx-users] periodic improper dihedral

[Mark Abraham]

Hi,

All that depends on is the atom types, so something there must not be
matching properly.

Mark

On Thu, 17 Dec 2015 10:15 Eric Smoll  wrote:

> Thank you Mark,
>
> We are having difficulty adding new parameters to the oplsaa forcefield in
> "share/gromacs.top." We have a "[ dihedraltypes ]" directive where I add
> fourier dihedral parameters (function type 5) and a "[ dihedraltypes ]"
> directive where I add periodic improper dihedrals (function type 4). We
> have itp/top files that contain two corresponding "[ dihedrals ]"
> directive.
>
> Grompp is complaining that "No default proper/improper dihedral type."
> Grompp also complains when the improper terms are represented with a proper
> dihedral (function type 2).
>
> Do you have any idea how I could trouble shoot this problem?
>
> Best,
> Eric
>
> On Wed, Dec 16, 2015 at 4:54 PM, Mark Abraham 
> wrote:
>
> > Yes
> >
> > On Thu, 17 Dec 2015 05:39 Eric Smoll  wrote:
> >
> > > Hello GROMACS users,
> > >
> > > I have a question about specifying periodic improper dihedrals in
> > GROMACS.
> > >
> > > In the GROMACS manual (chapter 5, table 5.5), the parameters of the
> > > periodic improper dihedral are listed as follows:
> > >
> > > phi_s ( deg ); k_phi (kJ mol^-1); multiplicity
> > >
> > > In the GROMACS manual (chapter 4, equation 4.60), the form of the
> > periodic
> > > improper dihedral is specified as
> > >
> > > V_d( phi_ijkl ) = k_phi ( 1 - cos(n*phi - phi_s))
> > >
> > > Am I correct in assuming that "n" shown is the "multiplicity" listed
> > above?
> > >
> > > Best,
> > > Eric
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
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> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
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Re: [gmx-users] System blowing up in Gromacsv5.0.5 but not in v4.5.4

[Justin Lemkul]

On 12/16/15 12:08 AM, NISHA Prakash wrote:

Dear Justin,

I am simulating a protein ligand complex. The protein co-ordinate file that
I have taken is an output of the simulation of the protein alone in
Gromacs-v5.0.5. The topology and the co-ordinates are fine. I am still
facing this problem wherein I get the LINCS warning for only the protein
atoms. The ligand also is fine.


If the protein fails, you have a problem somewhere.  That's either topology 
(unlikely), coordinates (probable), or .mdp (most probable).  You said in your 
earlier message that energy minimization failed, which points to coordinates 
being the problem.



Like I mentioned before, I do not have this problem when I use the
Gromacs-4.5.4 where I have used the same co-ordinate file with different
ligands and same parameter file.



If you're comparing a protein-ligand complex in 5.0.5 against different 
complexes in 4.5.4, that is a meaningless comparison.  It's apples and oranges. 
 If the same input coordinates and input .mdp files run in 4.5.4 and fail in 
5.0.5, that might be something to look into.  But the general advice applies 
here - either way you're using outdated software, so if something is failing, 
upgrade to the latest version and try again.


-Justin


Kindly let me know how to resolve the issue.

Thanking you in anticipation.

Nisha




On Wed, Dec 16, 2015 at 12:26 AM, Justin Lemkul  wrote:




On 12/15/15 8:42 AM, NISHA Prakash wrote:


Hi all,

I am trying to simulate a protein using similar parameters as in the
tutorial - Protein ligand by Justin Lemkul.

I am facing a problem wherein the protein simulation is exploding only in
this version - Gromacs-v5.0.5 but not in the older version Gromacs-v4.5.4.

The warning message is as follows

---
There were 4 inconsistent shifts. Check your topology

Steepest Descents:
 Tolerance (Fmax)   =  1.0e+03
 Number of steps=5

WARNING: Listed nonbonded interaction between particles 1312 and 1315
at distance 4.728 which is larger than the table limit 2.000 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.

ATOM   1312  O   TYR A 207
ATOM   1315  CD1 TYR A 207
-



---
em_real.mdp file

; LINES STARTING WITH ';' ARE COMMENTS
title = Minimization ; Title of run

; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0   ; Stop minimization when the maximum force < 10.0 kJ/mol
emstep  = 0.01  ; Energy step size
nsteps = 5   ; Maximum number of (minimization) steps to perform
energygrps = Protein ; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist= 1; Frequency to update the neighbor list and long range
forces
cutoff-scheme   = Verlet
ns_type= grid ; Method to determine neighbor list (simple, grid)
rlist= 1.0 ; Cut-off for making neighbor list (short range forces)
coulombtype= PME ; Treatment of long range electrostatic interactions
rcoulomb= 1.0 ; long range electrostatic cut-off
rvdw= 1.0 ; long range Van der Waals cut-off
pbc= xyz ; Periodic Boundary Conditions




The initial minimization step itself fails.



If minimization fails, you have a problem with the topology or
coordinates. Perhaps you got a bit lucky with some quirk of an algorithmic
difference in the old version that is failing here.

-Justin

I have tried to simulate a minimized structure as well, I still encounter

the same problem.

I would appreciate any help in this regard.
I would also like to know if this means, that the results from the older
version of gromacs reliable?

Thanking you in anticipation

Nisha



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

Re: [gmx-users] bond constraints: which distance is constrained?

[Vitaly V. Chaban]

ok

thank you




On Wed, Dec 16, 2015 at 11:33 AM, Justin Lemkul  wrote:

>
>
> On 12/16/15 8:29 AM, Vitaly V. Chaban wrote:
>
>> In bond constraints (all-bonds; LINCS...), does it constrain an initial
>> bond length (as in GRO) or an equilibrium bond length (as in ITP)?
>>
>> My tests reveal the constrained distance is taken from ITP, which is
>> somehow counter-intuitive to me.
>>
>>
> The constraint length is the equilibrium bond length as specified in the
> topology.  It's the same thing with applying a bond potential; the
> reference value is taken from the force field, not the geometry you
> supply.  Constraints convert those bonds (with specified equilibrium
> length) to a rigid entity.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
>
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Re: [gmx-users] MD production

[Justin Lemkul]

On 12/16/15 8:47 AM, mihammad roos wrote:

Hi everybody,


I’ve generated initial structure of my system by ambertoolsand convert the 
topology and coordinate files to Gromacs format by using parmEdto do the rest 
of simulation. Now, I’ve done the energy minimization andequilibration after 
that when I use the command “gmx_mpi grompp -f md.mdp -cnpt.gro -t npt.cpt -p 
gromacs.top -o md_0_1.tpr” for MD production I get thefollowing lines:



Ignoring obsolete mdp entry 'title'



Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5#

Setting the LD random seed to 4106683940

Generated 300 of the 300 non-bonded parameter combinations

Generating 1-4 interactions: fudge = 0.5

Generated 300 of the 300 1-4 parameter combinations

Excluding 3 bonded neighbours molecule type 'system1'

turning all bonds into constraints...

Excluding 3 bonded neighbours molecule type 'Na+'

turning all bonds into constraints...

Excluding 3 bonded neighbours molecule type 'Cl-'

turning all bonds into constraints...

Excluding 3 bonded neighbours molecule type 'WAT'

turning all bonds into constraints...

Removing all charge groups because cutoff-scheme=Verlet

Analysing residue names:

There are:20Protein residues

There are:27Ion residues

There are: 13766 Water residues

Analysing Protein...

Analysing residues not classified as Protein/DNA/RNA/Waterand splitting into 
groups...

.

.

.

Fatal error:

41734 atoms are not part of any of the T-Coupling groups

For more information and tips for troubleshooting, pleasecheck the GROMACS

website at http://www.gromacs.org/Documentation/Errors

---



Halting program gmx_mpi



gcq#27: "A Man Needs a Maid" (N. Young)



--

MPI_ABORT was invoked on rank 0 in communicatorMPI_COMM_WORLD

with errorcode -1.



NOTE: invoking MPI_ABORT causes Open MPI to kill all MPIprocesses.

You may or may not see output from other processes,depending on

exactly when Open MPI kills them.

--


My pdb file is consisted of 41734 atoms. I don’t know whatis wrong with my 
files. Can you please help me?




The error is obvious:

41734 atoms are not part of any of the T-Coupling groups

Set tc-grps appropriately.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] MD production

[mihammad roos]

Hi everybody,


I’ve generated initial structure of my system by ambertoolsand convert the 
topology and coordinate files to Gromacs format by using parmEdto do the rest 
of simulation. Now, I’ve done the energy minimization andequilibration after 
that when I use the command “gmx_mpi grompp -f md.mdp -cnpt.gro -t npt.cpt -p 
gromacs.top -o md_0_1.tpr” for MD production I get thefollowing lines:


 
Ignoring obsolete mdp entry 'title'


 
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5#

Setting the LD random seed to 4106683940

Generated 300 of the 300 non-bonded parameter combinations

Generating 1-4 interactions: fudge = 0.5

Generated 300 of the 300 1-4 parameter combinations

Excluding 3 bonded neighbours molecule type 'system1'

turning all bonds into constraints...

Excluding 3 bonded neighbours molecule type 'Na+'

turning all bonds into constraints...

Excluding 3 bonded neighbours molecule type 'Cl-'

turning all bonds into constraints...

Excluding 3 bonded neighbours molecule type 'WAT'

turning all bonds into constraints...

Removing all charge groups because cutoff-scheme=Verlet

Analysing residue names:

There are:    20    Protein residues

There are:    27    Ion residues

There are: 13766 Water residues

Analysing Protein...

Analysing residues not classified as Protein/DNA/RNA/Waterand splitting into 
groups...

.

.

.

Fatal error:

41734 atoms are not part of any of the T-Coupling groups

For more information and tips for troubleshooting, pleasecheck the GROMACS

website at http://www.gromacs.org/Documentation/Errors

---


 
Halting program gmx_mpi


 
gcq#27: "A Man Needs a Maid" (N. Young)


 
--

MPI_ABORT was invoked on rank 0 in communicatorMPI_COMM_WORLD 

with errorcode -1.


 
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPIprocesses.

You may or may not see output from other processes,depending on

exactly when Open MPI kills them.

--


My pdb file is consisted of 41734 atoms. I don’t know whatis wrong with my 
files. Can you please help me?


 
Thank you, Mohammad.

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[gmx-users] bond constraints: which distance is constrained?

[Vitaly V. Chaban]

In bond constraints (all-bonds; LINCS...), does it constrain an initial
bond length (as in GRO) or an equilibrium bond length (as in ITP)?

My tests reveal the constrained distance is taken from ITP, which is
somehow counter-intuitive to me.
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Re: [gmx-users] bond constraints: which distance is constrained?

[Justin Lemkul]

On 12/16/15 8:29 AM, Vitaly V. Chaban wrote:

In bond constraints (all-bonds; LINCS...), does it constrain an initial
bond length (as in GRO) or an equilibrium bond length (as in ITP)?

My tests reveal the constrained distance is taken from ITP, which is
somehow counter-intuitive to me.



The constraint length is the equilibrium bond length as specified in the 
topology.  It's the same thing with applying a bond potential; the reference 
value is taken from the force field, not the geometry you supply.  Constraints 
convert those bonds (with specified equilibrium length) to a rigid entity.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] Range of block lengths in gmx energy error estimate only gives one value

[Barnett, James W]

Good morning,

With gmx energy one can specify a range of block lengths to use for the error
estimate using "-nbmin" and "-nbmax". When I specify a range I still only get
one estimate. I would have expected a different estimate for each block length
in the range to be printed to the screen. I'm not understanding what value is
being printed in this case of specifying the range. If someone can give some
insight, that would be helpful.

Thanks,
Wes

-- 
James "Wes" Barnett, Ph.D. Candidate
Louisiana Board of Regents Fellow

Chemical and Biomolecular Engineering
Tulane University
341-B Lindy Boggs Center for Energy and Biotechnology
6823 St. Charles Ave
New Orleans, Louisiana 70118-5674
jbarn...@tulane.edu
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[gmx-users] viscosity using green-kubo

[Gmx QA]

Dear gmx-users

I sent mail a couple days ago about viscosity calculations, but no-one
answered so maybe it was too lengthy, so better luck this time I hope.

I want to calculate viscosity using Green-Kubo formalism, and have run a
box with tip3p waters for 100 ps in NVE, saving data every 1 fs.

For green-kubo, I then first use gmx energy to get (one of) the
off-diagonal elements in the pressure tensor (Pxy in this case)

$ gmx energy -f nve_prod.edr -o nve_prod_pressure_tensor_pxy.xvg

Then, I use gmx analyze to calculate the auto-correlation function of the
Pxy pressure component

$ gmx analyze -f nve_prod_pressure_tensor_pxy.xvg -ac
nve_prod_pressure_tensor_pxy_acf.xvg -nonormalize

And then again gmx analyze to integrate it.
$ gmx analyze -f nve_prod_pressure_tensor_pxy_acf.xvg -integrate

That gives me :
Calculating the integral using the trapezium rule
Integral 1  1940.24341  +/-0.0

Which I then plug into the green-kubo formula
eta = V/(kB*T)* int(…) = …=

For my V=1.59e-26 m^3, T=303 K and with kB=1.38e-23 I get eta = 0.0074

Now, I am not sure about units, or about the validity of this answer. I
tried changing the unit of the pressure from bar to pascal by multiplying
with 10, but the results makes equally less sense.

I have also read about averaging over several of the off-diagonal pressure
tensor components, which I could try, but is there anything fundamental
that I am missing above?

Hope for better luck with some answers this time!
/PK
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Re: [gmx-users] viscosity using green-kubo

[David van der Spoel]

On 16/12/15 15:42, Gmx QA wrote:

Dear gmx-users

I sent mail a couple days ago about viscosity calculations, but no-one
answered so maybe it was too lengthy, so better luck this time I hope.

I want to calculate viscosity using Green-Kubo formalism, and have run a
box with tip3p waters for 100 ps in NVE, saving data every 1 fs.

For green-kubo, I then first use gmx energy to get (one of) the
off-diagonal elements in the pressure tensor (Pxy in this case)

$ gmx energy -f nve_prod.edr -o nve_prod_pressure_tensor_pxy.xvg

Then, I use gmx analyze to calculate the auto-correlation function of the
Pxy pressure component

$ gmx analyze -f nve_prod_pressure_tensor_pxy.xvg -ac
nve_prod_pressure_tensor_pxy_acf.xvg -nonormalize

And then again gmx analyze to integrate it.
$ gmx analyze -f nve_prod_pressure_tensor_pxy_acf.xvg -integrate

That gives me :
Calculating the integral using the trapezium rule
Integral 1  1940.24341  +/-0.0

Which I then plug into the green-kubo formula
eta = V/(kB*T)* int(…) = …=

For my V=1.59e-26 m^3, T=303 K and with kB=1.38e-23 I get eta = 0.0074

Now, I am not sure about units, or about the validity of this answer. I
tried changing the unit of the pressure from bar to pascal by multiplying
with 10, but the results makes equally less sense.

I have also read about averaging over several of the off-diagonal pressure
tensor components, which I could try, but is there anything fundamental
that I am missing above?

Hope for better luck with some answers this time!
/PK


Have you tried gmx energy -vis ?

--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] Range of block lengths in gmx energy error estimate only gives one value

[David van der Spoel]

On 16/12/15 15:58, Barnett, James W wrote:

Good morning,

With gmx energy one can specify a range of block lengths to use for the error
estimate using "-nbmin" and "-nbmax". When I specify a range I still only get
one estimate. I would have expected a different estimate for each block length
in the range to be printed to the screen. I'm not understanding what value is
being printed in this case of specifying the range. If someone can give some
insight, that would be helpful.

Thanks,
Wes

This could well be a missing feature. I'm working on a patch for more 
solid energy analysis, https://gerrit.gromacs.org/#/c/4310/


--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] Viscosity of water from gmx tcaf

[Gmx QA]

No one that can comment on this? The very least on what data should be
fitted in visco_k.xvg to get the viscosity.

/PK

2015-12-15 10:14 GMT+01:00 Gmx QA :

> Dear users
>
> I am trying to teach myself how to calculate the viscosity of different
> simulations from gmx tcaf, and to that end I made a test system with a box
> of about 4000 water molecules, so that I can see if I can get a viscosity
> that matches that of water.
>
> I have read some mails on this list, and in particular the Berk Hess paper
> about various methods to calculate viscosity in gromacs, but I have some
> additional questions.
>
> From the help-text for gmx tcaf:
> The k-dependent viscosities in the -ov file should be fitted to eta(k) =
> eta_0
> (1 - a k^2) to obtain the viscosity at infinite wavelength.
>
> This is my command line for running gmx tcaf:
> $ gmx tcaf -f run.trr -s run.tpr -ov
>
> which gives me the visc_k.xvg file.
>
> I then tried to fit the data (per above) using xmgrace to y = a0 * (1 - a1
> * y * y), and get a0 = 0.41*10^-3 kg /m*s, which after unit conversion
> seems to be too low? (wikipedia says viscosity of water is 0.001 kg /m *s.
>
> On the other hand, gmx tcaf also says:
>
> When the box is cubic, one can use the option -oc, which averages the
> TCAFs over all k-vectors with the same length. This results in more
> accurate TCAFs. Both the cubic TCAFs and fits are written to -oc The cubic
> eta estimates are also written to -ov.
>
> Since I have a cubic box, I run
> $ gmx tcaf -f run.trr -s run.tpr -ov -oc
>
> which gives me another visc_k,xvg file with some (fitted?) data in it.
> What is this data?
> The following is also printed to stdout
>
> Averaged over k-vectors:
> k  1.273  tau  1.860  Omega  1.790  eta  0.14901 10^-3 kg/(m s)
> k  1.801  tau  1.133  Omega  2.061  eta  0.14087 10^-3 kg/(m s)
> k  2.206  tau  0.420  Omega  0.799  eta  0.09827 10^-3 kg/(m s)
> k  2.547  tau  0.340  Omega  0.599  eta  0.06810 10^-3 kg/(m s)
>
> Does gromacs somehow already compute the viscosity at "infinite
> wavelength"?, or am i missing something.
>
> I'd really, really appreciate some help here.
>
> Best
> /PK
>
>
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