Re: [gmx-users] how to make a porcupine plot?

[Justin A. Lemkul]

AntonioLeung wrote:

Hi, all,
I am newcomer of gmx, and I want to know how to make a porcupine plot 
after a essential MD. I found it looks nicer than linear interpolations 
between two extremes.

Thanks in advance!



There are not tools in Gromacs to do such a thing, but a simple Google search 
will turn up a number of external software/servers that can.  For example, the 
first Google hit:


http://s12-ap550.bioch.ox.ac.uk:8078/dynamite_html/dynatraj_splash_v1.5.html

-Justin


Atonio



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Justin A. Lemkul
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ICTAS Doctoral Scholar
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] how to make a porcupine plot?

[AntonioLeung]

Hi, all,
I am newcomer of gmx, and I want to know how to make a porcupine plot after a 
essential MD. I found it looks nicer than linear interpolations between two 
extremes.
Thanks in advance!

Atonio-- 
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Re: [gmx-users] g_msd => The MSD and periodic boundary condition

[Justin A. Lemkul]

Chih-Ying Lin wrote:





Hi With the periodic boundary condition, all the recorded coordinates of 
the atom are within the simulation box. To calculate the MSD, the 
movement of the center mass of the molecules between this time step with 
the next time step is calculated without considering the periodic 
boundary condition. But all the recorded coordinates of the atom are 
within the simulation box after considering the periodic boundary condition.




Does g_msd remove the effect of the periodic boundary condition ?


Yes.

So, how can I remove the periodic boundary condition to get the truly 
movement of the atoms between the two time steps ? Thank you Lin


No need.  See above.

-Justin









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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] g_msd => The MSD and periodic boundary condition

[Chih-Ying Lin]

Hi With the periodic boundary condition, all the recorded coordinates of the
atom are within the simulation box. To calculate the MSD, the movement of
the center mass of the molecules between this time step with the next time
step is calculated without considering the periodic boundary condition. But
all the recorded coordinates of the atom are within the simulation box after
considering the periodic boundary condition.



Does g_msd remove the effect of the periodic boundary condition ?
So, how can I remove the periodic boundary condition to get the truly
movement of the atoms between the two time steps ? Thank you Lin
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RE: [gmx-users] User results for another run

[Dallas B. Warren]

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

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the only tool you own is a hammer, every problem begins to resemble
a nail. 

> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of Jack Shultz
> Sent: Friday, 20 November 2009 9:56 AM
> To: Discussion list for GROMACS users
> Subject: [gmx-users] User results for another run
> 
> I must have asked this before but I'm trying find the answer again. If
> I want to use the results from mdrun for another run following the
> first time interval, what do I need to do?
> 
> --
> Jack
> 
> http://drugdiscoveryathome.com
> http://hydrogenathome.org
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Re: [gmx-users] User results for another run

[Justin A. Lemkul]

Jack Shultz wrote:

I must have asked this before but I'm trying find the answer again. If
I want to use the results from mdrun for another run following the
first time interval, what do I need to do?



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

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] User results for another run

[Jack Shultz]

I must have asked this before but I'm trying find the answer again. If
I want to use the results from mdrun for another run following the
first time interval, what do I need to do?

-- 
Jack

http://drugdiscoveryathome.com
http://hydrogenathome.org
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RE: [gmx-users] How to check for bad contacts

[Dallas B. Warren]

When you try to minimise, it will typically tell you the worst offending
atoms in your system.  Which you can then check visually using VMD etc
and try and work out why it is an issue.  Then you can adjust how the
system was set up to fix the issue.

 

Also, if you just look at the system visually (though can be an issue
with larger systems) if there is something that is really out of place,
it can be easy to spot.  Such as two molecules too close, interlocked,
or severely distorted.

 

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the only tool you own is a hammer, every problem begins to resemble
a nail. 

 

From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Lum Nforbi
Sent: Friday, 20 November 2009 9:19 AM
To: gmx-users@gromacs.org
Subject: [gmx-users] How to check for bad contacts

 

Hello,

How do you check for bad contacts in a system that cannot be minimized?

Thanks,
Lum 

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[gmx-users] How to check for bad contacts

[Lum Nforbi]

Hello,

How do you check for bad contacts in a system that cannot be minimized?

Thanks,
Lum
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RE: [gmx-users] Hydrated radius of ions

[Dallas B. Warren]

g_rdf ?

 

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the only tool you own is a hammer, every problem begins to resemble
a nail. 

 

From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Manik Mayur
Sent: Friday, 20 November 2009 2:10 AM
To: Discussion list for GROMACS users
Subject: [gmx-users] Hydrated radius of ions

 

Hi,

Is there any gromacs utility to calculate the hydrated radius of ions?

Thanks,

Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
INDIA

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[gmx-users] Problem with Gromacs-CPMD

[jorge_quintero]

Dear all,

I'm running some simulations using Gromacs/CPMD but it doesn't continue
during QMCONTINUE file lecture.  See below:


 EXTERNAL ENERGY=  5.867019924829098E-002  AU
 REAL TOTAL ENERGY  =  -97.3517503273190   AU

   ATOM  COORDINATESGRADIENTS (-FORCES)
   1  C  7.2410  9.0551  9.8394   7.709E-02 -3.867E-02 -2.540E-02
  
  12 Cu  7.2410 14.2141  6.4946  -5.854E-04 -6.465E-03  1.232E-02
  INTERFACE| FORCES WRITTEN TO FILE

 RESTART INFORMATION WRITTEN ON FILE  ./RESTART.1

 ===
  INTERFACE| WAIT FOR CONTINUE-FILE
 ./QMCONTINUE  <===   Here!

At this point my simulations don't continue.  A appreciate your support!!


Jorge R. Quintero
Universidad Industrial de Santander
Bucaramanga, Santander - Colombia

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Re: [gmx-users] 6-31G** for Gromacs

[Mark Abraham]

ilona.bal...@bioquant.uni-heidelberg.de wrote:



Hi Gerrit,

I would like to use 6-31G** for my QMMM-calculation. Since sulfur is 
part of my QM system, I consider that a sensible thing to do. 
Unfortunately, it is not implemented in Gromacs, so I tried to add that 
bit myself.


Here's the point where I got stuck:
 src/mdlib/qm_gaussian.c translates the basis set is converted via 
"ivec" to some number format for gaussian (line 75-84). How did you get 
the numbers in {} and what do they mean?


Follow the usage of the data in that file - search for basisset, and 
then the data structure to which the integers get mapped. It seems clear 
to me they're being used to create a Gaussian route. The correct values 
for other basis sets will be determined by Gaussian, so try its 
documentation.



The other part where I am insecure is include/types/enums.h, line 199-203:

enum {
  eQMbasisSTO3G, eQMbasisSTO3G2, eQMbasis321G,
  eQMbasis321Gp, eQMbasis321dGp, eQMbasis621G,
  eQMbasis631G, eQMbasis631Gp, eQMbasis631dGp,
  eQMbasis6311G, eQMbasisNR
};

Obviously, names are just listed here, so I think of just adding 
"eQMbasis631Gdp" for 6-31G** which is equal to 6-31G(d,p). Would that 
conflict with eQMbasis631dGp which stands for 6-31+G* ?


Sort of. You can see from the usage of eQMbasisNR here and everywhere 
else (grep is your friend) that the lengths of various data structures 
must match. This is a recurring GROMACS-ism. If you extend all such by 
inserting an entry corresponding to 6-31G** I suspect it will just work.


Mark
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[gmx-users] 6-31G** for Gromacs

[ilona . baldus]

Hi Gerrit,

I would like to use 6-31G** for my QMMM-calculation. Since sulfur is  
part of my QM system, I consider that a sensible thing to do.  
Unfortunately, it is not implemented in Gromacs, so I tried to add  
that bit myself.


Here's the point where I got stuck:
 src/mdlib/qm_gaussian.c translates the basis set is converted via  
"ivec" to some number format for gaussian (line 75-84). How did you  
get the numbers in {} and what do they mean?


The other part where I am insecure is include/types/enums.h, line 199-203:

enum {
  eQMbasisSTO3G, eQMbasisSTO3G2, eQMbasis321G,
  eQMbasis321Gp, eQMbasis321dGp, eQMbasis621G,
  eQMbasis631G, eQMbasis631Gp, eQMbasis631dGp,
  eQMbasis6311G, eQMbasisNR
};

Obviously, names are just listed here, so I think of just adding  
"eQMbasis631Gdp" for 6-31G** which is equal to 6-31G(d,p). Would that  
conflict with eQMbasis631dGp which stands for 6-31+G* ?


Thanks in advance,

Best wishes, Ilona



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Re: [gmx-users] FEP with bond formation, pair problem

[Jochen Hub]

David van der Spoel wrote:

Berk Hess wrote:

Hi,

There are automatically different, since they are based on the A and 
B state charges

and the A and B state atom types.


But the problem is more complicated:

Let's say there is a Butane radical C4H9. that you want to bond to 
another butane radical to form octane (C8H18). Then the interactions 
that are non-bonded in the A state are excluded in the B state and 
replaced by pair interactions.


Is this supported in some way?


Actually for the LJ part that is supported. The solution is to turn the 
normal non-bonded LJ in part A into pairs and explicitly give the 
standart sigma/epsion as A, and zero sigma/epsilon (for 1-2 and 1-3 in 
B), or scaled (for 1-4 in B) as B state parameters.


So far so good. But can the same be done for the colomb 1-4 interactions 
in the B state? The problem arises since the 1-4 coulomb interactions 
are scaled down by 1.2 in the AMBER FF, so I need different 1-4 coulomb 
interactions in A and B.


In principle that problem should be in any FEP calculation which 
includes the formation of a bond.


Jochen










Berk

 > Date: Thu, 19 Nov 2009 16:15:52 +0100
 > From: joc...@xray.bmc.uu.se
 > To: gmx-users@gromacs.org
 > Subject: [gmx-users] FEP with bond formation, pair problem
 >
 > Hi,
 >
 > how can I use different coulomb 1-4 interactions in the A and B 
state.

 > The Manual just says
 >
 > [ pairs ] : LJ and Coulomb 1-4 interactions
 >
 > but, I far as I could see, did not give an example how the coulomb 
1-4

 > interaction can be explicitly given.
 >
 > Thanks a lot for any help,
 >
 > Jochen
 >
 >
 > --
 > ---
 > Dr. Jochen Hub
 > Molecular Biophysics group
 > Dept. of Cell & Molecular Biology
 > Uppsala University. Box 596, 75124 Uppsala, Sweden.
 > Phone: +46-18-4714451 Fax: +46-18-511755
 > ---
 >
 > --
 > gmx-users mailing list gmx-users@gromacs.org
 > http://lists.gromacs.org/mailman/listinfo/gmx-users
 > Please search the archive at http://www.gromacs.org/search before 
posting!

 > Please don't post (un)subscribe requests to the list. Use the
 > www interface or send it to gmx-users-requ...@gromacs.org.
 > Can't post? Read http://www.gromacs.org/mailing_lists/users.php


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---
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Molecular Biophysics group
Dept. of Cell & Molecular Biology
Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4714451 Fax: +46-18-511755
---

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Re: [gmx-users] FEP with bond formation, pair problem

[David van der Spoel]

Berk Hess wrote:

Hi,

There are automatically different, since they are based on the A and B 
state charges

and the A and B state atom types.


But the problem is more complicated:

Let's say there is a Butane radical C4H9. that you want to bond to 
another butane radical to form octane (C8H18). Then the interactions 
that are non-bonded in the A state are excluded in the B state and 
replaced by pair interactions.


Is this supported in some way?





Berk

 > Date: Thu, 19 Nov 2009 16:15:52 +0100
 > From: joc...@xray.bmc.uu.se
 > To: gmx-users@gromacs.org
 > Subject: [gmx-users] FEP with bond formation, pair problem
 >
 > Hi,
 >
 > how can I use different coulomb 1-4 interactions in the A and B state.
 > The Manual just says
 >
 > [ pairs ] : LJ and Coulomb 1-4 interactions
 >
 > but, I far as I could see, did not give an example how the coulomb 1-4
 > interaction can be explicitly given.
 >
 > Thanks a lot for any help,
 >
 > Jochen
 >
 >
 > --
 > ---
 > Dr. Jochen Hub
 > Molecular Biophysics group
 > Dept. of Cell & Molecular Biology
 > Uppsala University. Box 596, 75124 Uppsala, Sweden.
 > Phone: +46-18-4714451 Fax: +46-18-511755
 > ---
 >
 > --
 > gmx-users mailing list gmx-users@gromacs.org
 > http://lists.gromacs.org/mailman/listinfo/gmx-users
 > Please search the archive at http://www.gromacs.org/search before 
posting!

 > Please don't post (un)subscribe requests to the list. Use the
 > www interface or send it to gmx-users-requ...@gromacs.org.
 > Can't post? Read http://www.gromacs.org/mailing_lists/users.php


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Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se
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[gmx-users] Re: Force Fields

[Vitaly V. Chaban]

The selection of FF depends on what you study. Perhaps, none of them
will be useful for you. The existing ones differ at least by the
procedures if generation although many parameters are very close.

>
> What are the main differences between the force fields used in gromacs?  In
> which scenarios are each force field better to use?
>
> Chanel
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RE: [gmx-users] FEP with bond formation, pair problem

[Berk Hess]

Hi,

There are automatically different, since they are based on the A and B state 
charges
and the A and B state atom types.

Berk

> Date: Thu, 19 Nov 2009 16:15:52 +0100
> From: joc...@xray.bmc.uu.se
> To: gmx-users@gromacs.org
> Subject: [gmx-users] FEP with bond formation, pair problem
> 
> Hi,
> 
> how can I use different coulomb 1-4 interactions in the A and B state. 
> The Manual just says
> 
> [ pairs ] : LJ and Coulomb 1-4 interactions
> 
> but, I far as I could see, did not give an example how the coulomb 1-4 
> interaction can be explicitly given.
> 
> Thanks a lot for any help,
> 
> Jochen
> 
> 
> -- 
> ---
> Dr. Jochen Hub
> Molecular Biophysics group
> Dept. of Cell & Molecular Biology
> Uppsala University. Box 596, 75124 Uppsala, Sweden.
> Phone: +46-18-4714451 Fax: +46-18-511755
> ---
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
  
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Re: [gmx-users] covariance

[Tsjerk Wassenaar]

Hi Morteza,

To me, your initial question seemed to relate to scaling/constraining
the covariances. But I also take most any opportunity to warn people
not to think too ligthly about PCA :) You can use xpm2ps to combine
the matrices and recolorize according to the range of the combined
set.

Hope it helps,

Tsjerk

2009/11/19 Morteza Khabiri :
> Dear Tsjerk
>
> Thanks for your help and reply. I thing my question was not clear.
> I want to compare  2 covariance map. but in one map the red colour shows e.g
> 1 nm^2 fluctuation and in other map the red colour shows e.g 0.5 nm^2
> fluctuation. I wanted that both map be in the same scale of colour
> intensity. I mean in both red color max range be 1 nm^2 till the
> comparison of 2 map on a basis of colour intensity be easier. I hope I
> could make my question clear.
>
>
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Medicinal Chemist
Neuropharmacologist
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Re: [gmx-users] How to make carbon nanotube infinite?

[Justin A. Lemkul]

Cun Zhang wrote:



I mean, I make  the distance of the top ( or bottom ) C atoms in CNT and 
the corresponding edge of the box equals the length of a C-C bond( about 
0.142nm ).


OK, that sounds reasonable, but did you define the periodic bonds appropriately? 
 Your original question was that you did not know how to do that.


I use a (16,0) CNT with 832 atoms ( length 5.472nm).I use the following 
command to produce a CNT-water system


 >editconf -f CNT.pdb -o -box 3.8 3.8 5.614

No velocities found
system size :  1.270  1.270  5.472 (nm)
center  : -0.000  0.000  2.736 (nm)
box vectors :  0.000  0.000  0.000 (nm)
box angles  :   0.00   0.00   0.00 (degrees)
box volume  :   0.00   (nm^3)
shift   :  1.900  1.900  0.071 (nm)
new center  :  1.900  1.900  2.807 (nm)
new box vectors :  3.800  3.800  5.614 (nm)
new box angles  :  90.00  90.00  90.00 (degrees)
new box volume  :  81.07   (nm^3)

 >genbox -cp out -cs -p CNT -o b4em.pdb

Output configuration contains 7513 atoms in 2228 residues
Volume : 81.0662 (nm^3)
Density: 1026.51 (g/l)
Number of SOL molecules:   2227  


Processing topology
Adding line for 2227 solvent molecules to topology file (CNT.top)

 >pymol b4em.pdb # I write a python script to remove the SOL molecules 
in the Carbon nanotube.


Are there any solvent molecules interfering with the cross-boundary bonds?


 >editconf -f b4em.pdb -o b4em.gro -box 3.8 3.8 5.614 #rebuild the box.


Why are you doing this?


 >grompp -v -f em -c b4em -o em -p CNT -maxwarn 5


Are there warnings you are ignoring by using -maxwarn 5?


NOTE 1 [file CNT.top, line unknown]:
  The largest charge group contains 32 atoms.
  Since atoms only see each other when the centers of geometry of the charge
  groups they belong to are within the cut-off distance, too large charge
  groups can lead to serious cut-off artifacts.
  For efficiency and accuracy, charge group should consist of a few atoms.
  For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.



Pay attention to this note.  A charge group of 32 atoms is huge.



Checking consistency between energy and charge groups...
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 32x32x48, spacing 0.119 0.119 0.117
Estimate for the relative computational load of the PME mesh part: 0.41
This run will generate roughly 15 Mb of data
writing run input file...

There was 1 note

Back Off! I just backed up em.tpr to ./#em.tpr.1#

gcq#87: "It's Because Of the Metric System" (Pulp Fiction)

 >mdrun -v -s em
Back Off! I just backed up md.log to ./#md.log.1#
Getting Loaded...
Reading file em.tpr, VERSION 4.0.5 (single precision)
Loaded with Money




OK, so what happens?  Does the EM converge, or does the minimization fail?


Back Off! I just backed up traj.trr to ./#traj.trr.1#

Back Off! I just backed up traj.xtc to ./#traj.xtc.1#

Back Off! I just backed up ener.edr to ./#ener.edr.1#
starting mdrun 'CNT in water'
5 steps, 25.0 ps.
step 0Segmentation fault



Instant crashing indicates the structure is unstable, and that EM likely wasn't 
sufficient.



THE b4em.gro file is like:


There is no useful information in the .gro file, and nothing out of the ordinary 
in the .mdp file.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] FEP with bond formation, pair problem

[Jochen Hub]

Hi,

how can I use different coulomb 1-4 interactions in the A and B state. 
The Manual just says


[ pairs ] : LJ and Coulomb 1-4 interactions

but, I far as I could see, did not give an example how the coulomb 1-4 
interaction can be explicitly given.


Thanks a lot for any help,

Jochen


--
---
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Molecular Biophysics group
Dept. of Cell & Molecular Biology
Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4714451 Fax: +46-18-511755
---

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Re: [gmx-users] How to make carbon nanotube infinite?

[Cun Zhang]

Justin, thanks for your reply. By the way, your GMX tutorials is great!

I post the gro file and mdp file at the end.


On Thu, Nov 19, 2009 at 10:09 PM, Justin A. Lemkul  wrote:

>
> Not possible, Gromacs 4.1 hasn't been released :)  If you're using version
> 4.0.1, you shouldn't, because it has a nasty bug that affects performance
> very severely.


I'm using GMX 4.0.5, not 4.1. Sorry! :)


>  I set the box size larger than CNT's length a C-C bond(half up and half
>> down).
>>  If I don't do a EM, it will crumble. But if I do it,it can't satisfy that
>> the box size is larger then CN't length a C-C bond.
>>
>
> I don't understand this.  Are you getting any error messages?  Screen and
> log output are more useful in most cases.
>

I mean, I make  the distance of the top ( or bottom ) C atoms in CNT and the
corresponding edge of the box equals the length of a C-C bond( about 0.142nm
).
I use a (16,0) CNT with 832 atoms ( length 5.472nm).I use the following
command to produce a CNT-water system

>editconf -f CNT.pdb -o -box 3.8 3.8 5.614

No velocities found
system size :  1.270  1.270  5.472 (nm)
center  : -0.000  0.000  2.736 (nm)
box vectors :  0.000  0.000  0.000 (nm)
box angles  :   0.00   0.00   0.00 (degrees)
box volume  :   0.00   (nm^3)
shift   :  1.900  1.900  0.071 (nm)
new center  :  1.900  1.900  2.807 (nm)
new box vectors :  3.800  3.800  5.614 (nm)
new box angles  :  90.00  90.00  90.00 (degrees)
new box volume  :  81.07   (nm^3)

>genbox -cp out -cs -p CNT -o b4em.pdb

Output configuration contains 7513 atoms in 2228 residues
Volume : 81.0662 (nm^3)
Density: 1026.51 (g/l)
Number of SOL molecules:   2227

Processing topology
Adding line for 2227 solvent molecules to topology file (CNT.top)

>pymol b4em.pdb # I write a python script to remove the SOL molecules in the
Carbon nanotube.
>editconf -f b4em.pdb -o b4em.gro -box 3.8 3.8 5.614 #rebuild the box.
>grompp -v -f em -c b4em -o em -p CNT -maxwarn 5
NOTE 1 [file CNT.top, line unknown]:
  The largest charge group contains 32 atoms.
  Since atoms only see each other when the centers of geometry of the charge
  groups they belong to are within the cut-off distance, too large charge
  groups can lead to serious cut-off artifacts.
  For efficiency and accuracy, charge group should consist of a few atoms.
  For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.


Checking consistency between energy and charge groups...
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 32x32x48, spacing 0.119 0.119 0.117
Estimate for the relative computational load of the PME mesh part: 0.41
This run will generate roughly 15 Mb of data
writing run input file...

There was 1 note

Back Off! I just backed up em.tpr to ./#em.tpr.1#

gcq#87: "It's Because Of the Metric System" (Pulp Fiction)

>mdrun -v -s em
Back Off! I just backed up md.log to ./#md.log.1#
Getting Loaded...
Reading file em.tpr, VERSION 4.0.5 (single precision)
Loaded with Money


Back Off! I just backed up traj.trr to ./#traj.trr.1#

Back Off! I just backed up traj.xtc to ./#traj.xtc.1#

Back Off! I just backed up ener.edr to ./#ener.edr.1#
starting mdrun 'CNT in water'
5 steps, 25.0 ps.
step 0Segmentation fault

THE b4em.gro file is like:

GROtesk MACabre and Sinister
 7243
1UNK CX1   2.508   1.929   0.069
1UNK CX2   2.496   2.053   0.141
1UNK CX3   2.460   2.172   0.069
1UNK CX4   2.401   2.282   0.141
.
.
1UNK CX  828   1.424   1.480   5.541
1UNK CX  829   1.520   1.401   5.469
1UNK CX  830   1.630   1.342   5.541
1UNK CX  831   1.749   1.306   5.469
1UNK CX  832   1.873   1.294   5.541
2SOL OW  833   0.542   1.304   1.163
2SOLHW1  834   0.449   1.297   1.126
2SOLHW2  835   0.553   1.393   1.207
3SOL OW  836   1.716   0.647   0.854
3SOLHW1  837   1.749   0.741   0.854
3SOLHW2  838   1.767   0.593   0.920
.
.
 2137SOL OW 7238   0.214   2.438   5.002
 2137SOLHW1 7239   0.252   2.379   5.074
 2137SOLHW2 7240   0.254   2.412   4.914
 2138SOL OW 7241   3.736   2.968   4.022
 2138SOLHW1 7242   3.835   2.957   4.013
 2138SOLHW2 7243   3.696   2.882   4.054
   3.8   3.8   5.61400

The following is my mdp file:
; VARIOUS PREPROCESSING OPTIONS
title= Yo
cpp  = /usr/bin/cpp
include  =
define   =

; RUN CONTROL PARAMETERS
integrator   = md
; Start time and timestep in ps
tinit= 0
dt   = 0.0005
nsteps   = 5
; For exact run continuation or redoing part of a run
init_step= 0
; mode for center of mass motion removal
comm-mode= Linear
; numb

[gmx-users] H-bonds in water + alcohol mixture

[Nuno Garrido]

Dear all,

I'm trying to evaluate the number of H-bonds in a 150 alcohol (TraPPE)
+ 57 water (SPC/E) molecules mixture.

>From rdf analysis I can observe that the most prominent peak is
related to OW-OW group, followed by OW-OH group and finally OH-OH
group.
OW = water oxygen
OH = alcohol oxygen.

>From g_hbond analysis I have calculated (at fixed cutoff = 0.35 nm +
angle = 30º) the following average number of hydrogen bonds per time
step:
Water - Water = 36.53 --> 36.53 / 57= 0.64 per molecule
Water - Alcohol   = 106.13 --> 106.13/207 = 0.513
Alcohol - Alcohol = 96.23 --> 96.23/150= 0.64

I was expected to observe the same trend in both rdf and number of
H-bonds... Someone has some clue about what I am doing wrong ?

Thanks in advance
Nuno Garrido
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[gmx-users] Hydrated radius of ions

[Manik Mayur]

Hi,

Is there any gromacs utility to calculate the hydrated radius of ions?

Thanks,

Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
INDIA
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[gmx-users] covariance

[Morteza Khabiri]

Dear Tsjerk

Thanks for your help and reply. I thing my question was not clear.
I want to compare  2 covariance map. but in one map the red colour shows e.g
1 nm^2 fluctuation and in other map the red colour shows e.g 0.5 nm^2
fluctuation. I wanted that both map be in the same scale of colour
intensity. I mean in both red color max range be 1 nm^2 till the
comparison of 2 map on a basis of colour intensity be easier. I hope I
could make my question clear.


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Re: [gmx-users] Force Fields

[Justin A. Lemkul]

Smith, Chanel Chonda wrote:

What are the main differences between the force fields used in gromacs?  In
which scenarios are each force field better to use?
 


I think this question is best addressed by a thorough examination of the 
literature and the various textbooks that exist regarding simulation methodology.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] Force Fields

[Smith, Chanel Chonda]

What are the main differences between the force fields used in gromacs?  In
which scenarios are each force field better to use?
 
Chanel
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Re: [gmx-users] covariance

[Tsjerk Wassenaar]

Hi Morteza,

Your question suggests a lack of understanding of the principles (not
principals) of covariance analysis. It is probably best to read a bit
more on the background of this technique, until you realize what it
is, what it can do, and what it can't. There are a number of
discussions archived on the matter. I also briefly touch the topic in
the tutorial at http://nmr.chem.uu.nl/~tsjerk/course/molmod/
(analysis). But the best references to get to understand the technique
are probably from statistics. Googling will yield plenty of documents.
If you feel that I'm off with this reply, then please give a more
detailed account of what you intend to do and how you think covariance
analysis will help you achieving your aim.

Hope it helps,

Tsjerk

2009/11/19 Morteza Khabiri :
> Dear gmxuser
>
> I want to compare a dimer covariance which was already run in 2 different
> situation. The problem is that the scale of produced covariance (which
> produced by -xpma) in 2 case is different e.g the scale for one of them
> start from -0.18 to 0.05 and other -0.15 to 0.052. Is there any
> possibility to calculate covarianse in the same scale?
>
> thanks
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist
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Re: [gmx-users] How to make carbon nanotube infinite?

[Justin A. Lemkul]

Cun Zhang wrote:

Hi,gmx users,
I want to set CNT infinite in the system of CNT and water.  I'm using 
GMX 4.1,so I have set pbc=xyz, periodic_molecules=yes in mdp file.


Not possible, Gromacs 4.1 hasn't been released :)  If you're using version 
4.0.1, you shouldn't, because it has a nasty bug that affects performance very 
severely.


I set the box size larger than CNT's length a C-C bond(half up and half 
down).
 If I don't do a EM, it will crumble. But if I do it,it can't satisfy 
that the box size is larger then CN't length a C-C bond.


I don't understand this.  Are you getting any error messages?  Screen and log 
output are more useful in most cases.



I have searched google and gmx mail list, but still can't solve it .

I found that GMX online document about Carbon 
Nanotube(http://www.gromacs.org/index.php?title=Documentation/How-tos/Carbon_Nanotube)

say,

Be absolutely sure that the "terminal" carbon atoms are sharing a bond 
in the topology file.


I don't understand it.How should I do?



Make sure there is a bond in your topology between the appropriate atoms at one 
"edge" of the box to the appropriate atoms at the other "edge" of the box.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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: SV: SV: SV: [gmx-users] Hydrogen bonding

[Justin A. Lemkul]

Sarah Witzke wrote:



-Original Message- From: gmx-users-boun...@gromacs.org on behalf of
Justin A. Lemkul Sent: Thu 19-11-2009 02:09 To: Gromacs Users' List Subject:
Re: SV: SV: SV: [gmx-users] Hydrogen bonding


Sarah Witzke wrote:



Sarah Witzke wrote:




ARRGH, I'm sorry, things went too quick :-( So the lifetime in average
per hbond is 628.571 ps?


Yes, per the calculation.  For a bit more about the analysis, see the
"Please read and cite" notices, as well as this thread:

http://lists.gromacs.org/pipermail/gmx-users/2009-February/039955.html

The note about the correlation function would imply that the correlation 
function itself has not converged until its value is < 0.001.  This is

usually a result of insufficient data, either the length of the
simulation, or number of frames analyzed (based on the spacing of the
frames).

Hmm, so using 120 ns simulation from a standard .xtc file (timestep of 10
ps) is not long enough. Perhabs I should try the original .trr file...
The .xtc file I'm using only contains DMPC and the small molecule, no
solvent - I can't see this would make a difference in this case, am I
right?


The correlation will depend on how much the interactions are changing over
the period you analyzed.  If you are analyzing a small molecule and DMPC,
water should not matter.

I have now tried with the full length (220 ns) .trr file and the -ac output
still prints a warning:

ACF 106/106 Normalization for c(t) = 1.23261 for gh(t) = 5.58815e-05

WARNING: Correlation function is probably not long enough because the
standard deviation in the tail of C(t) > 0.001 Tail value (average C(t)
over second half of acf): 0.000172327 +/- 0.00277407

In your opinion, does this mean that I cannot trust the value of the
lifetime, since the correlation function is not converging?



I'm not entirely sure.  Please see the posts from David in the thread I 
referenced before about some potential issues with the ACF in the g_hbond 
calculation.  I assume you are using version 4.0.x?


I'm using version 4.0.4 for consistency. I have read the posts from you and
David van der Spoel
(http://lists.gromacs.org/pipermail/gmx-users/2009-February/039955.html) as
well as the article given by g_hbond. I guess this auto correlation function
and the lifetime derived by this is... well, I'm not sure I trust it enough
to put it in a paper - especially since my acf doesn't converge (which I
still find strange, it should not matter that I have only saved coordinates
every 10 ps in my .trr file when using the Luzar acfs-approached, right?).

The - hbm option i g_hbond creates a matrix that can be converted to a .eps
file by usin xpm2ps. The picture obtained is nice looking but lacking in some
of the information I would like to derive. I would like to know how many
frames each hbond exists (another way to consider lifetime). I have opened
the .xpm file in a text editor and there are a long list of lines starting
similar to tgis one: /* x-axis:  10 100010 100020 Can I somehow obtain
the number of frames for each hbond from this?



Either write a script that counts the number of instances of "o" characters per 
line in the .xpm file, then divide by the total number of frames, or iteratively 
call g_hbond for each of the H-bonds that were initially identified (and whose 
indices are now written to hbond.ndx from -hbn).  The latter approach will still 
require some post-processing, of course, since each output .xvg file will be a 
series of either 0 or 1, indicating the absence or presence of that particular 
H-bond.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] How to make carbon nanotube infinite?

[Cun Zhang]

Hi,gmx users,
I want to set CNT infinite
in the system of CNT and water.  I'm using GMX 4.1,so I have set pbc=xyz,
periodic_molecules=yes in mdp file.
I set the box size larger than CNT's length a C-C bond(half up and half
down).
 If I don't do a EM, it will crumble. But if I do it,it can't satisfy
that the box size is larger then CN't length a C-C bond.
I have searched google and gmx mail list,
but still can't solve it .

I found that GMX online document about Carbon Nanotube(http://www.gromacs.org/index.php?title=Documentation/How-tos/Carbon_Nanotube)
say,

Be absolutely sure that the
"terminal" carbon atoms are sharing a bond in the topology
file.

I don't understand it.How should I do?

Thanks!

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RE: SV: SV: SV: [gmx-users] Hydrogen bonding

[Sarah Witzke]

-Original Message-
From: gmx-users-boun...@gromacs.org on behalf of Justin A. Lemkul
Sent: Thu 19-11-2009 02:09
To: Gromacs Users' List
Subject: Re: SV: SV: SV: [gmx-users] Hydrogen bonding
 

Sarah Witzke wrote:
>  
> 
> Sarah Witzke wrote:
> 
> 
> 
>> ARRGH, I'm sorry, things went too quick :-( So the lifetime in average per 
>> hbond is 628.571 ps?
>>
> 
> Yes, per the calculation.  For a bit more about the analysis, see the "Please
> read and cite" notices, as well as this thread:
> 
> http://lists.gromacs.org/pipermail/gmx-users/2009-February/039955.html
> 
>> The note about the correlation function would imply that the correlation
>> function itself has not converged until its value is < 0.001.  This is 
>> usually a
>> result of insufficient data, either the length of the simulation, or number 
>> of
>> frames analyzed (based on the spacing of the frames).
>>
>> Hmm, so using 120 ns simulation from a standard .xtc file (timestep of 10 
>> ps) is not long enough. Perhabs I should try the original .trr file... The 
>> .xtc file I'm using only contains DMPC and the small molecule, no solvent - 
>> I can't see this would make a difference in this case, am I right?
>>
> 
> The correlation will depend on how much the interactions are changing over the
> period you analyzed.  If you are analyzing a small molecule and DMPC, water
> should not matter.
> 
> I have now tried with the full length (220 ns) .trr file and the -ac output 
> still prints a warning:
> 
>   ACF 106/106
>   Normalization for c(t) = 1.23261 for gh(t) = 5.58815e-05
> 
>   WARNING: Correlation function is probably not long enough
>   because the standard deviation in the tail of C(t) > 0.001
>   Tail value (average C(t) over second half of acf): 0.000172327 +/- 
> 0.00277407
> 
> In your opinion, does this mean that I cannot trust the value of the 
> lifetime, since the correlation function is not converging?
> 

  I'm not entirely sure.  Please see the posts from David in the thread I
  referenced before about some potential issues with the ACF in the g_hbond
  calculation.  I assume you are using version 4.0.x?

I'm using version 4.0.4 for consistency. I have read the posts from you and 
David van der Spoel 
(http://lists.gromacs.org/pipermail/gmx-users/2009-February/039955.html) as 
well as the article given by g_hbond. I guess this auto correlation function 
and the lifetime derived by this is... well, I'm not sure I trust it enough to 
put it in a paper - especially since my acf doesn't converge (which I still 
find strange, it should not matter that I have only saved coordinates every 10 
ps in my .trr file when using the Luzar acfs-approached, right?). 

The - hbm option i g_hbond creates a matrix that can be converted to a .eps 
file by usin xpm2ps. The picture obtained is nice looking but lacking in some 
of the information I would like to derive. I would like to know how many frames 
each hbond exists (another way to consider lifetime). I have opened the .xpm 
file in a text editor and there are a long list of lines starting similar to 
tgis one: 
  /* x-axis:  10 100010 100020 
Can I somehow obtain the number of frames for each hbond from this?

Thank you very much again!

-Justin

> Thank you!
> 
> 
> I have conducted the analysis on the 
> -Justin
> 
> --
> 
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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 mailing listgmx-users@gromacs.org
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> 
> 

-- 


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] covariance

[Morteza Khabiri]

Dear gmxuser

I want to compare a dimer covariance which was already run in 2 different
situation. The problem is that the scale of produced covariance (which
produced by -xpma) in 2 case is different e.g the scale for one of them
start from -0.18 to 0.05 and other -0.15 to 0.052. Is there any
possibility to calculate covarianse in the same scale?

thanks

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Re: [gmx-users] Adding ions

[Amir Marcovitz]

Hi,

Make sure you do specify the explicit names of the topology and structure
file. in the mannual they omit the suffix of the file.
for the purpose of rigourism -  this is the line i'm using:

genion -pname Na+ -nname Cl- -o file_ionized.gro  -conc  0.2  -p
topol.top

On Tue, Nov 17, 2009 at 1:56 AM, Arden Perkins  wrote:

> I am an undergraduate student and I am still learning to use GROMACS. When
> I add my ions to the solution (using genion) by the procedure described in
> the funnel web spider tutorial the .gro and .top files do not match. I tried
> subtracting solvent molecules but they still dont match and I can't
> continue. What am I doing wrong?
>
> Thanks!
>
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