RE: [gmx-users] Viscosity in PE

[Alessandro Mattozzi]

Thanx!

Alessandro Mattozzi
M.Phil., Ph.D. student
Dept. of Fibre and Polymer Technology
Royal Institute of Technology
Stockholm, Sweden



-Original Message-
From: [EMAIL PROTECTED] on behalf of Berk Hess
Sent: Fri 9/8/2006 8:34 AM
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Viscosity in PE
 



>From: David van der Spoel <[EMAIL PROTECTED]>
>Reply-To: Discussion list for GROMACS users 
>To: Discussion list for GROMACS users 
>Subject: Re: [gmx-users] Viscosity in PE
>Date: Thu, 07 Sep 2006 19:36:34 +0200
>
>Esther Caballero-Manrique wrote:
>>You can calculate it from the velocity autocorrelation function, which can 
>>be calculated using the g_velacc. The friction can be calculated from the 
>>integral of the velocity autocorrelation function (friction=3KbT/(integral 
>>of vacf)) and then the viscosity can be calculated using Stoke's equation 
>>(friction=6 x PI x visc x radius). But you need to have saved the 
>>velocities fairly often (say every 5 fs?). This came up recently in the 
>>mailing lists, you can search the velocity autocorrelation function. This 
>>method integrates the integral at time infinite (ie, see Morriss and 
>>Evan's book /Statistical Mechanics of Nonequilibrium Liquids, /now on the 
>>web @ http://rsc.anu.edu.au/~evans/evansmorrissbook.htm) which might or 
>>might not be a good approximation for your system. Otherwise you can do 
>>more sophisticated methods such as those outlined in chapter 6 of the 
>>manual.
>>Hope it helps,
>>Esther
>
>An alternative method that is implemented requires non-equibrium 
>simulations. Check out
>
>@Article{Hess2002b,
>   author = {B. Hess},
>   title =  {Determining the shear viscosity of model liquids from 
>molecular simulation},
>   journal ={J. Chem. Phys.},
>   year =   2002,
>   volume = 116,
>   pages =  {209-217}
>}
>
>you have to set cos_acceleration in the mdp to e.g. 0.1 nm/ps^2

In Gromacs viscosity calculations can be done with several methods,
all of which are described in the paper mentioned above.

But for PE-1000 it is not that straightforward as for a simple liquid.
The system has very long relaxation times and the viscosity will be
very non-linear in the shear rate.
You should read some literature on viscosity calculations in polymer melts.

Berk.


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Re: [gmx-users] Viscosity in PE

[Berk Hess]

From: David van der Spoel <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users 
To: Discussion list for GROMACS users 
Subject: Re: [gmx-users] Viscosity in PE
Date: Thu, 07 Sep 2006 19:36:34 +0200

Esther Caballero-Manrique wrote:
You can calculate it from the velocity autocorrelation function, which can 
be calculated using the g_velacc. The friction can be calculated from the 
integral of the velocity autocorrelation function (friction=3KbT/(integral 
of vacf)) and then the viscosity can be calculated using Stoke's equation 
(friction=6 x PI x visc x radius). But you need to have saved the 
velocities fairly often (say every 5 fs?). This came up recently in the 
mailing lists, you can search the velocity autocorrelation function. This 
method integrates the integral at time infinite (ie, see Morriss and 
Evan's book /Statistical Mechanics of Nonequilibrium Liquids, /now on the 
web @ http://rsc.anu.edu.au/~evans/evansmorrissbook.htm) which might or 
might not be a good approximation for your system. Otherwise you can do 
more sophisticated methods such as those outlined in chapter 6 of the 
manual.

Hope it helps,
Esther


An alternative method that is implemented requires non-equibrium 
simulations. Check out


@Article{Hess2002b,
  author =   {B. Hess},
  title = 	 {Determining the shear viscosity of model liquids from 
molecular simulation},

  journal =  {J. Chem. Phys.},
  year = 2002,
  volume =   116,
  pages ={209-217}
}

you have to set cos_acceleration in the mdp to e.g. 0.1 nm/ps^2


In Gromacs viscosity calculations can be done with several methods,
all of which are described in the paper mentioned above.

But for PE-1000 it is not that straightforward as for a simple liquid.
The system has very long relaxation times and the viscosity will be
very non-linear in the shear rate.
You should read some literature on viscosity calculations in polymer melts.

Berk.


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Re: [gmx-users] Re: Simulation problem with extended membrane system!

[liu xin]

Hi ChrisThank you for your note!According to your suggestion, I did a energy minimization and then a MDS with "freezegrps=SOL, freezedim=N, N, Y", the rest of the system were simulated with no constraint. This time I use semiisotropic pressure coupling with tau_p=5. The system will be equilibrated with water constrained for 1ns, do you think it's enough?
The reason why I want to extend the system is because that I've got a GPCR, and I want to simulate it in a DPPC membrane environment, but the z dimension of the membrane, downloaded from Dr. Tielman's websit,  was not large enough, when I align the protein to the z axis of the membrane I find the two ends of the protein are poking out of both water layers.
Back to the previous question, after solvate the lipids in water, can I remove the water placed in the membrane with excel instead of script? Cause with editconf we can know the z dimension of the lipids_only system, let's say 6, so if I center the whole system with 0 0 0, the water molecules with z coordinates below 3 and above -3 will be excluded. If I'm right, I think excel can do it too, or the scripts have some advantages?
Thank you againOn 9/8/06, [EMAIL PROTECTED]
 <[EMAIL PROTECTED]> wrote:
Having actually looked back at my notes, here is what I did to extend pope.pdbinto a larger system. However, the suggestion that I posted last time should
work just as well.1. Remove all waters2. Duplicate the box until your heart's content. Make it larger than youactually want because the box will collapse to some extent.3. MD with Z-only posre on lipid head groups (X and Y force components = zero).
This step must be done with constant pressure (In this procedure, make sure touse isotropic pressure coupling so that the box max and min z don't come intocontact with the membrane).NOTE for step 3: It is assumed that your edges line up with each other. Load the
system into vmd and show periodic unit cells to make sure. If they line uppoorly then I would find a new starting PDB. However, pope.pdb lines up well.4. Adjust the z-dimension to what you want it to be, center your membrane in the
z if you want to.5. solvate the system.6. Remove any waters that were placed within the membrane7. energy minimize8. posre run as before to allow the water to adjust to the membrane surfaces.However, during this run (and all the rest of the steps) I use semiisotropic
Pcoupling.9. equilibration phase without any position restraints10. production run.If you are going to add protein, you could do that with the results of step 4since most procedures involve stripping out any waters anyway.
Again, the procedure that I outlined previously should work, but I have nottested that procedure, only this one.___gmx-users mailing list

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Re: [gmx-users] how to exclude some atoms from coulomb interaction calculation?

[David van der Spoel]

Cherry Y. Yates wrote:

Dear all,

I did a massive MD simulation of nanostructure. In my calculation, over 
80% atoms have zero charge and the main CPU time is devoted to Coulomb 
interaction. I wonder if anyone knows how to exclude these neutral atoms 
from Coublomb interaction so that a lot of CPU time will be saved.


They are excluded already. GROMACS does not compute nonbonded 
interactions when the result is zero. This can be due to charges or LJ 
parameters being zero.




Many thanks,

Cherry

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--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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[gmx-users] why the mdrun stop

[zzhwise1]

 
hello ,everyone
  I have two problems:
(1)my model is compost of 36 long chain of CH3(CH2)14COOH  ,and use the frocefiled of ffgmx,
but the mdrun can only going to the 2th step,and the some chains change large 
(2)can this program do the nanotribology of   monolayer?
thanks advanced!
wait for your answer!
    your friend
 
 

	买 这 些 让 女 友 很 兴 奋 ( 图 ) 
	
	 真 会 过 日 子 ! 一 个 月 收 入 5800 漂 亮 MM 的 感 性  生 活 ( 组 图 )


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Re: [gmx-users] why the mdrun stop

[David van der Spoel]

zzhwise1 wrote:
 
hello ,everyone

  I have two problems:
(1)my model is compost of 36 long chain of CH3(CH2)14COOH  ,and use the 
frocefiled of ffgmx,
but the mdrun can only going to the 2th step,and the some chains change 
large

(2)can this program do the nanotribology of   monolayer?
thanks advanced!
wait for your answer!



check your starting structure. start with one molecule, minimize, do MD 
and then go to 36 molecules.



your friend
 
 








买 这 些 让 女 友 很 兴 奋 ( 图 )
真 会 过 日 子 ! 一 个 月 收 入 5800 漂 亮 MM 的 感 性 生 活 ( 组 图 ) 
 






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--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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Re: [gmx-users] why the mdrun stop

[Itamar Kass]

Shalom,

You did not mention if you did energy minimization or other preliminary steps
before your MD. If not, this might solve the problem.

Best,
Itamar.

Quoting zzhwise1 <[EMAIL PROTECTED]>:

>
> hello ,everyone
>   I have two problems:
> (1)my model is compost of 36 long chain of CH3(CH2)14COOH  ,and use the
> frocefiled of ffgmx,
> but the mdrun can only going to the 2th step,and the some chains change large
> (2)can this program do the nanotribology of   monolayer?
> thanks advanced!
> wait for your answer!
> your friend
>
>




===
| Itamar Kass
| The Alexander Silberman
| Institute of Life Sciences
| Department of Biological Chemistry
| The Hebrew University, Givat-Ram
| Jerusalem, 91904, Israel
| Tel: +972-(0)2-6585194
| Fax: +972-(0)2-6584329
| Email: [EMAIL PROTECTED]



This message was sent using IMP, the Internet Messaging Program.
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[gmx-users] genion causing atom to be in multiple T-Coupling groups

[Una Bjarnadottir]

Dear Users,

I'm trying to neutralize my system adding 3 Cl ions with genion and when 
running grompp again with the new generated .gro file I get this error:

Fatal error: Atom 33000 in multiple T-Coupling groups (15 and 1)

which is the last water atom (total in system 33003) and groups 15 and 1 
are Cl and protein groups if I on the other hand do not neutralize the 
system the run goes fine!  So there is something wrong with how the 
genion works for me.  I followed the tutorial and chose the SOL group 
and water molecules were replaced by the Cl ions.  Than I modifyed the 
.top file and took 3 sol molecules and added the 3 ions.

_*
*_Best regards for any help, Una Bjarnadottir
_*
.top before:
*_; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound#mols
Protein_E   1
Protein_I1
Protein_A  1
SOL 9719
_*.top after*_
; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound#mols
Protein_E   1
Protein_I1
Protein_A  1
SOL 9716
CL-3

_*These are my commands:*_
   #
   #Run grompp
   #
   emfile_mdpfile='em.mdp'
   emout='em_out.mdp'
   structure_file='em.tpr'
   os.system('/usr/local/bin/grompp -f '+emfile_mdpfile+ ' -po ' 
+emout+ ' -c ' +water_grofile+ ' -o ' +structure_file+ ' -p ' +topologyfile)


   #
   #Run genion
   #
   ion_out='ion.gro'
   os.system('/usr/local/bin/genion -s '+structure_file+ ' -o ' 
+ion_out+ ' -nname Cl -nn 3')


   #
   #Run grompp
   #
   structure_file_after_genion='em_genion.tpr'
   os.system('/usr/local/bin/grompp -f '+emfile_mdpfile+ ' -po ' 
+emout+ ' -c ' +ion_out+ ' -o ' +structure_file_after_genion+ ' -p ' 
+topologyfile)



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[gmx-users] Splitting one run

[Martin Höfling]

Hi there,

I heard that there's an unofficial script to split one run in several small 
ones. Anyone of you remembers the topic so that I can search for it?

Regards
Martin
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[Fwd: Re: Re: [gmx-users] why the mdrun stop]

[David van der Spoel]

 Original Message 
Subject:Re: Re: [gmx-users] why the mdrun stop
Date:   Fri, 8 Sep 2006 21:58:02 +0800 (CST)
From:   zzhwise1 <[EMAIL PROTECTED]>
To: david van der spoel <[EMAIL PROTECTED]>
References: <[EMAIL PROTECTED]>
<[EMAIL PROTECTED]>



I try 3 long chains
but I don't konw why the program do not allow the bond to rotation 30 or
more degree?
does it the case of the wrong ff or wrong integrate ?








-原始邮件-
发件人:"David van der Spoel"
发送时间:2006-09-08 19:05:02
收件人:"Discussion list for GROMACS users"
抄送:(无)
主题:Re: [gmx-users] why the mdrun stop


zzhwise1 wrote:

>

> hello ,everyone

>   I have two problems:

> (1)my model is compost of 36 long chain of CH3(CH2)14COOH  ,and
use the

> frocefiled of ffgmx,

> but the mdrun can only going to the 2th step,and the some chains
change

> large

> (2)can this program do the nanotribology of   monolayer?

> thanks advanced!

> wait for your answer!





check your starting structure. start with one molecule, minimize, do MD

and then go to 36 molecules.



> your friend

>

>

>

>

>

>

>

>

>

> 买 这 些 让 女 友 很 兴 奋 ( 图 )

> 真 会 过 日 子 ! 一 个 月 收 入 5800 漂 亮 MM 的 感 性 生 活 ( 组
图 )

> ,597,58&cid=29985,198,1&sid=32501&show=ignore&url=http://www.taobao.com/vertical/lady/pro.php>


>

>

>

>


>

> ___

> gmx-users mailing listgmx-users@gromacs.org

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--

David.



David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,

Dept. of Cell and Molecular Biology, Uppsala University.

Husargatan 3, Box 596,  75124 Uppsala, Sweden

phone:  46 18 471 4205  fax: 46 18 511 755

[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se




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买 这 些 让 女 友 很 兴 奋 ( 图 )
真 会 过 日 子 ! 一 个 月 收 入 5800 漂 亮 MM 的 感 性 生 活 ( 组 图 )



-- 
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se



CHOXIUGAI.mdp
Description: Binary data
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[gmx-users] Re: Simulation problem with extended membrane system!

[chris . neale]

>According to your suggestion, I did a energy minimization and then a MDS
>with "freezegrps=SOL, freezedim=N, N, Y", the rest of the system were
>simulated with no constraint. This time I use semiisotropic pressure
>coupling with tau_p=5. The system will be equilibrated with water
>constrained for 1ns, do you think it's enough?

It will be more than enough. Use vmd to watch the trajectory. It's important 
actually look at the structures.

>The reason why I want to extend the system is because that I've got a GPCR,
>and I want to simulate it in a DPPC membrane environment, but the z
>dimension of the membrane, downloaded from Dr. Tielman's websit,  was not
>large enough, when I align the protein to the z axis of the membrane I find
>the two ends of the protein are poking out of both water layers.

In this case you may not need to extend the lipid. Why not just use editconf to 
increase the z dimension while keeping the x and y constant. Then insert your 
protein, re-solvate, re-equilibrate, and your into production. If your lipid 
takes up a maximum amout of space D in the xy-plane, then x and y need only be 
equal to [D + 2*max(LJ cutoff, Coulombic real-space cutoff) + some extra amount 
in case the protein fluctuations make it larger during the simulation].

>Back to the previous question, after solvate the lipids in water, can I
>remove the water placed in the membrane with excel instead of script? Cause
>with editconf we can know the z dimension of the lipids_only system, let's
>say 6, so if I center the whole system with 0 0 0, the water molecules with
>z coordinates below 3 and above -3 will be excluded. If I'm right, I think
>excel can do it too, or the scripts have some advantages?

Sure you can use excel, but I am not sure how that is going to affect your 
formatting or how gromacs responds to formatting (i.e. spaces / tabs / the 
number of each) So scrips have 2 advantages: 1)formatting is easily maintained, 
2)if you need to do it a second time you just type one command. After using 
excel (or a script) make sure to update you topology file to indicate the 
number 
of waters.

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[gmx-users] TFE .gro files

[Copps, Jeffrey]

Title: TFE .gro files







 Hello all,

 Does anyone have TFE (trifluoroethanol) .gro files that they might be willing to share?  Or, barring that, can anyone tell me how to create a solvent .gro file?

 Much thanks,

 Jeff Copps




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[gmx-users] Coulomb 1-4 interactions

[Jianhui Tian]

Hi gmx-users:
 
I am running a comparison between AMBER and Gromacs for a AOT system. First I created the AMBER force field and then transformed it to Gromacs force field. I did 1 step of MD respectively in AMBER and Gromacs with the same configuration. All the energy terms including bond, angle, dihedral, LJ (SR), LJ (14) and Coulomb (SR) are the same with each other between the two runs except the Coulomb (14) interaction. What might be the reason for this? I have totally no idea. Because the LJ (14) and Coulomb (14) calculation use the same 1-4 pairs in Gromacs, the LJ (14) is the same which means the 1-4 pairs are the same between AMBER and Gromacs. The Coulomb (SR) is the same which means the charges are the same between AMBER and Gromacs. (I also checked these two things explicitly between AMBER and Gromacs.) How could the Coulomb (14) be different then? Does any one have any idea about how the coulomb (14) interactions are calculated in AMBER and Gromacs? Thanks a lot.

 
Best Regards,
Justin
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Re: [gmx-users] Coulomb 1-4 interactions

[Ryogo Sugitani]

Justin,

What is your fudgeQQ value in ffamberXX.itp?
This value (I think the default is 0.8333) should be the reciprocal of 
scaling factor used in Amber's input file (I think the default is 1.200).
Check amber's manual specific parameter name for it. (I don't remember off my 
head right now.)

Best,

Ryogo

On Fri, 8 Sep 2006 13:26:45 -0400, Jianhui Tian wrote:
> Hi gmx-users:
>  
> I am running a comparison between AMBER and Gromacs for a AOT system. 
> First I created the AMBER force field and then transformed it to 
> Gromacs force field. I did 1 step of MD respectively in AMBER and 
> Gromacs with the same configuration. All the energy terms including 
> bond, angle, dihedral, LJ (SR), LJ (14) and Coulomb (SR) are the same 
> with each other between the two runs except the Coulomb (14) 
> interaction. What might be the reason for this? I have totally no 
> idea. Because the LJ (14) and Coulomb (14) calculation use the same 
> 1-4 pairs in Gromacs, the LJ (14) is the same which means the 1-4 
> pairs are the same between AMBER and Gromacs. The Coulomb (SR) is the 
> same which means the charges are the same between AMBER and Gromacs. 
> (I also checked these two things explicitly between AMBER and 
> Gromacs.) How could the Coulomb (14) be different then? Does any one 
> have any idea about how the coulomb (14) interactions are calculated 
> in AMBER and Gromacs? Thanks a lot.
>  
> Best Regards,
> Justin
> 
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Re: [gmx-users] Coulomb 1-4 interactions

[Mark Abraham]

> Hi gmx-users:
>
> I am running a comparison between AMBER and Gromacs for a AOT system.
> First
> I created the AMBER force field and then transformed it to Gromacs force
> field.

There are existing ports that you can find in the User Contributions
section of the GROMACS webpage. Comparing yours with theirs may well be
instructive for somebody.

> I did 1 step of MD respectively in AMBER and Gromacs with the same
> configuration. All the energy terms including bond, angle, dihedral, LJ
> (SR), LJ (14) and Coulomb (SR) are the same with each other between the
> two
> runs except the Coulomb (14) interaction. What might be the reason for
> this?

Various force fields routinely scale this interaction. Check the papers
that describe the implementation of the AMBER force field for information
here. Then read the GROMACS manual to work out how to implement the same.

> I have totally no idea. Because the LJ (14) and Coulomb (14) calculation
> use
> the same 1-4 pairs in Gromacs, the LJ (14) is the same which means the 1-4
> pairs are the same between AMBER and Gromacs. The Coulomb (SR) is the same
> which means the charges are the same between AMBER and Gromacs. (I also
> checked these two things explicitly between AMBER and Gromacs.) How could
> the Coulomb (14) be different then? Does any one have any idea about how
> the
> coulomb (14) interactions are calculated in AMBER and Gromacs? Thanks a
> lot.

See above - read the original papers.

Mark

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[gmx-users] can the GMX model the monolayer frict ion ?

[zzhwise1]

 
hello everyone 
    I want to know whether GMX can simulate the LB monolayer  or selfassemble monolayer on base ?if can not ,could advise one to me?
  thanks! 
 
 

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Re: [gmx-users] can the GMX model the monolayer frict ion ?

[Mark Abraham]

>
> hello everyone
> I want to know whether GMX can simulate the LB monolayer  or
> selfassemble monolayer on base ?if can not ,could advise one to me?
>   thanks!

Yes it is mathematically capable of doing that. You would know this, and a
whole lot more, if you read the GROMACS webpage thoroughly
http://www.gromacs.org/

Mark

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[gmx-users] LINCS warning

[Ragothaman Yennamalli]

Dear all,
I have a query,
1. Are two trajectories comparable if each one of them
has been run in a different version of gromacs? Eg,
v3.2 and v3.3.

Thanks in advance,
Regards,
Raghu

**
Y. M. Ragothaman,
Research Scholar,
Centre for Computational Biology and Bioinformatics,
School of Information Technology,
Jawaharlal Nehru University,
New Delhi - 110067.

Telephone: 91-11-26717568, 26717585
Facsimile: 91-11-26717586
**



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