RE: [gmx-users] g_energy

[Payman Pirzadeh]

Hello,
I am using gromacs 4.5.4. In g_energy I see an option about #surf*surfTen.
Could you please clarify how it is calculated? In a system with a protein
and water, what does it correspond to? 
Best,

Paymon

-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: March-29-12 7:23 PM
To: Acoot Brett; Discussion list for GROMACS users
Subject: Re: [gmx-users] protein melting experiment by GROMACS



Acoot Brett wrote:
> Dear All,
>  
> I remember before I have read a something on melting the protein from 
> a predefined starting temperature to a predefined end temperature by 
> MD, so that after the MD we can look at the whole process to see which 
> part of the protein unfold earlier, which part of the protein of the 
> protein unfold earlier. No I cannot find that introduction.
>  
> After we equilibriate the protein system, will you please tell me how 
> to define the temperature gradient from the start temperature to the 
> end temperature in the mdp file? Or do you have a protocol on it?
>  

See the manual regarding simulated annealing.

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Editing of the existing system

[James Starlight]

Dear Gromacs Users!


I have some system wich consist of protein in membrane-mimicking layer
surrounded by water. I want to modify my existing system by adding small
peptide fragment to this system. I want to dock this peptide to the some
part of my protein wich is situated  in the bottom water layer.

While doing such task I've aligned both of the components of new system in
one desired dimmension so as the consequence I have peptide.gro file in the
desired orientation relative to my system.

Now as I understood there are 2 possible ways

1- Manually copy_past peptide.gro into the system and run minimisation.

2- More accuracy- using genbox for such task

genbox -cp Gs.gro -cs system.gro -o new.gro

where Gs.gro is my peptide and system.gro is the system.

But when I've tried such task I've obtain only peptide as well as some
solvent ( small part of water) as the consequence. How I could fix it to
obtain desired system with the removed overlapping water with the new
peptide ? What are the additions tips could you provide me about such
docking ?

Thanks,

JAmes
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Re: [gmx-users] protein melting experiment by GROMACS

[Justin A. Lemkul]

Acoot Brett wrote:

Dear All,
 
I remember before I have read a something on melting the protein from a 
predefined starting temperature to a predefined end temperature by MD, 
so that after the MD we can look at the whole process to see which part 
of the protein unfold earlier, which part of the protein of the protein 
unfold earlier. No I cannot find that introduction.
 
After we equilibriate the protein system, will you please tell me how to 
define the temperature gradient from the start temperature to the end 
temperature in the mdp file? Or do you have a protocol on it?
 


See the manual regarding simulated annealing.

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] protein melting experiment by GROMACS

[Mark Abraham]

On 30/03/2012 12:11 PM, Acoot Brett wrote:

Dear All,
I remember before I have read a something on melting the protein from 
a predefined starting temperature to a predefined end temperature by 
MD, so that after the MD we can look at the whole process to see which 
part of the protein unfold earlier, which part of the protein of the 
protein unfold earlier. No I cannot find that introduction.
After we equilibriate the protein system, will you please tell me how 
to define the temperature gradient from the start temperature to the 
end temperature in the mdp file? Or do you have a protocol on it?




Simulated annealing. See manual and/or textbook material.

Mark
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[gmx-users] protein melting experiment by GROMACS

[Acoot Brett]

Dear All,
 
I remember before I have read a something on melting the protein from a 
predefined starting temperature to a predefined end temperature by MD, so that 
after the MD we can look at the whole process to see which part of the protein 
unfold earlier, which part of the protein of the protein unfold earlier. No I 
cannot find that introduction.
 
After we equilibriate the protein system, will you please tell me how to define 
the temperature gradient from the start temperature to the end temperature in 
the mdp file? Or do you have a protocol on it?
 
Cheers,
 
Fenghui-- 
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Re: [gmx-users] Not able to continue with Equilibration

[Mark Abraham]

On 30/03/2012 8:39 AM, francesca vitalini wrote:

Thank you Justin for your answer. I'm trying to add the position
restraints to my protein, but I have a problem. My topology is made of
a chain repeated twice and if I want to build the position restraints
through genrestr from a gro file, the numeration of the atoms would
put the 2 chains sequentially one after the other, but then the index
would be out of bounds;


As genrestr -h and the manual tells you (and as was discussed on this 
list a day or two ago), [position_restraints] apply to all copies of 
that [moleculetype]. So use genrestr on the first molecule only and you 
will have position restraints for both molecules for the price of one.



  if I try to generate the topology from x2top
it has been taking more than 6 hours and hasn't finish yet. If instead
I try to use the posre.itp built from pdb2gmx I still have the LINCS
warnings, even after changing rlist, rcoulomb and rvdw to 1. Any ideas
on a faster way to add my position restraints or how to solve the
LINCS error? Thank you very much.


Follow the advice here 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up


Mark
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Re: [gmx-users] About the function of "-v' in mdrun

[Peter C. Lai]

It's almost always a good idea to run with -v because it will output basic 
state information and time-to-completion estimates as your simulation runs. 
It prints to "standard out" so if launching mdrun from a script (like on a 
cluster), make sure the script captures the output to a file.

I find the data that -v outputs to be more useful in general than the extra
details found in the .log file.

On 2012-03-29 04:10:03PM -0700, Acoot Brett wrote:
> Dear All,
> 
> There is a tutorial says the function of "-v" in mdrun is to make the md 
> process visible in the screen, which is correct.
> 
> However from the introduction of mdrun in the new version of gromacs, it says 
> the function of "-v" is to make "noisy and loud".
> 
> Will you please tell me what is the meaning of "noisy and loud" here?
> 
> I am looking forward to getting your reply.
> 
> Cheers,
> 
> Acoot

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-- 
==
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Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
==

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RE: [gmx-users] About the function of "-v' in mdrun

[Dallas Warren]

Slang for “it says a lot”, being verbose (which is what –v means), lots of 
information printed out.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9903 9304
-
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 Acoot Brett
Sent: Friday, 30 March 2012 10:10 AM
To: Discussion list for GROMACS users
Subject: [gmx-users] About the function of "-v' in mdrun

Dear All,

There is a tutorial says the function of "-v" in mdrun is to make the md 
process visible in the screen, which is correct.

However from the introduction of mdrun in the new version of gromacs, it says 
the function of "-v" is to make "noisy and loud".

Will you please tell me what is the meaning of "noisy and loud" here?

I am looking forward to getting your reply.

Cheers,

Acoot


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[gmx-users] About the function of "-v' in mdrun

[Acoot Brett]

Dear All,

There is a tutorial says the function of "-v" in mdrun is to make the md 
process visible in the screen, which is correct.

However from the introduction of mdrun in the new version of gromacs, it says 
the function of "-v" is to make "noisy and loud".

Will you please tell me what is the meaning of "noisy and loud" here?

I am looking forward to getting your reply.

Cheers,

Acoot-- 
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Re: [gmx-users] How to read in mdcrd files to gromacs?

[Broadbent, Richard]

Dear Cat,

> Dear experts,
> 
> I am trying to do the following command:
> 
> /usr/local/gromacs/bin/g_covar_d -s test.pdb -f test.mdcrd -o -v
> 
If you are using -o & -v options you should specify files for them

> But the following error message is found:
> 
> ---
> Program g_covar_d, VERSION 4.5.5
> Source code file: trxio.c, line: 870
> 
> Fatal error:
> Not supported in read_first_frame: md0.mdcrd
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
> 
> What should I do next to solve this problem, I heard GROMACS can read mdcrd
> trajectory files from AMBER, right?
It can via VMD plugins:
http://www.gromacs.org/Documentation/How-tos/Using_VMD_plugins_to_read_traje
ctory_formats_not_native_to_GROMACS

Hope that's helpful

Richard
> 
> Best regards,
> 
> Cat
> 
>
> 
> 

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[gmx-users] Re: how to optimize hydrogen bonds before simulation?

[Dr. Vitaly V. Chaban]

>
> Hello:
>
>   I am wondering is it possible to optimize hydrogen bonds network
> before simulation? I've got some crystal solvent in the system and I
> would like to optimize the hbond network even before building a solvent
> system.

If you freeze all atoms which are not involved in H-bonds, the
coordinates of the remaining atoms will be optimized. Another question
is why you need that "before building a solvent".


Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA
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Re: [gmx-users] Not able to continue with Equilibration

[francesca vitalini]

Thank you Justin for your answer. I'm trying to add the position
restraints to my protein, but I have a problem. My topology is made of
a chain repeated twice and if I want to build the position restraints
through genrestr from a gro file, the numeration of the atoms would
put the 2 chains sequentially one after the other, but then the index
would be out of bounds; if I try to generate the topology from x2top
it has been taking more than 6 hours and hasn't finish yet. If instead
I try to use the posre.itp built from pdb2gmx I still have the LINCS
warnings, even after changing rlist, rcoulomb and rvdw to 1. Any ideas
on a faster way to add my position restraints or how to solve the
LINCS error? Thank you very much.
Francesca

2012/3/29 Justin A. Lemkul :
>
>
> francesca vitalini wrote:
>>
>> My minimization was done without any constraints. I'm starting using
>> constraints only in the nvt equilibration as I'm trying to equilibrate
>> my solvent, so, maybe here I'm being extremely naďve, but, shouldn't I
>>
>> avoid fixing the water in the nvt, as equilibrating it is exactly the
>> reason I'm running the nvt equilibration? Or am I misunderstanding
>> something?
>
>
> You should likely be restraining your protein, not the water.  Bad initial
> geometry (sometimes stuff survives EM) can give your structure a nasty kick
> that causes things to spin out of control.  Restraints on the protein
> mitigate these effects while the water relaxes.
>
> -Justin
>
>
>> Thanks
>> Francesca
>>
>>
>>
>> 2012/3/29  :
>>>
>>> I didn't follow this whole thread, but I sometimes need to turn off all
>>> constraints when doing minimization. In fact, for that reason I entirely
>>> stopped ever using restraints during energy minimization. In extreem
>>> cases,
>>> I have had success also by forcing the water to be flexible with a
>>> -DFLEXIBLE (or whatever is appropriate for your water model; check the
>>> .itp)
>>> statement in the .mdp file.
>>>
>>> Once EM is done, use rigid water and restraints and everything works out
>>> ok.
>>>
>>> Chris.
>>>
>>> -- original message --
>>>
>>> Hallo Felix,
>>> thank you for your answer. I tried the constraints = h-bonds but no
>>> change in the output. If I look at the step.pdb file that is produced
>>> after the running I have some strange outcome. For example some of my
>>> atoms are not recognized as part of my protein any more and my
>>> structure is destroied. Am I using some strange parameters for nvt
>>> without realizing it? I've started from the mdp file provided by the
>>> lysozyme tutorial non the Gromacs webpage.
>>> if anyone has any ideas it is more than welcome.
>>> Francesca
>>>
>>> integrator      = md            ; leap-frog integrator
>>> nsteps          = 1         ; 2 * 1 = 20 ps
>>> dt              = 0.002         ; 2 fs
>>> ; Output control
>>> nstxout         = 1             ; save coordinates every 0.2 ps
>>> nstvout         = 1             ; save velocities every 0.2 ps
>>> nstenergy       = 50            ; save energies every 0.2 ps
>>> nstlog          = 50            ; update log file every 0.2 ps
>>> ; Bond parameters
>>> unconstrained_start = no
>>> ;continuation   = no            ; first dynamics run
>>> constraint_algorithm = lincs    ; holonomic constraints
>>> constraints     = h-bonds       ; all bonds (even heavy atom-H bonds)
>>> constrained
>>> lincs_iter      = 1             ; accuracy of LINCS
>>> lincs_order     = 4             ; also related to accuracy
>>> ; Neighborsearching
>>> ns_type         = grid          ; search neighboring grid cells
>>> nstlist         = 5             ; 10 fs
>>> rlist           = 3.0           ; short-range neighborlist cutoff (in nm)
>>> rcoulomb        = 3.0           ; short-range electrostatic cutoff (in
>>> nm)
>>> rvdw            = 3.0           ; short-range van der Waals cutoff (in
>>> nm)
>>> ; Electrostatics
>>> coulombtype     = PME           ; Particle Mesh Ewald for long-range
>>> electrostatics
>>> pme_order       = 4             ; cubic interpolation
>>> fourierspacing  = 0.16          ; grid spacing for FFT
>>> ; Temperature coupling is on
>>> tcoupl          = berendsen     ; modified Berendsen thermostat
>>> tc-grps         = Protein Non-Protein   ; two coupling groups - more
>>> accurate
>>> tau_t           = 0.1 0.1       ; time constant, in ps
>>> ref_t           = 300 300               ; reference temperature, one
>>> for each group, in K
>>> ; Pressure coupling is off
>>> pcoupl          = no            ; no pressure coupling in NVT
>>> ; Periodic boundary conditions
>>> pbc             = xyz           ; 3-D PBC
>>> ; Dispersion correction
>>> DispCorr        = EnerPres      ; account for cut-off vdW scheme
>>> ; Velocity generation
>>> gen_vel         = yes           ; assign velocities from Maxwell
>>> distribution
>>> gen_temp        = 300           ; temperature for Maxwell distribution
>>> gen_seed        = -1            ; generate a random seed
>>>
>>>
>>>
>>> 2012/3/29 Rausch, Felix :

Re: [gmx-users] HB lifetime

[Erik Marklund]

29 mar 2012 kl. 18.47 skrev Nidhi Katyal:

> Dear All
> I would like to know the strength of the given bond by calculating the 
> lifetime of that bond.For the same reason i used:
> g_hbond -f *.xtc -s *.tpr -ac *.xvg -temp 300 -num *.xvg -life *.xvg
> and i got:
> TypeRate(1/ps)  Time(ps)  ...
> Forward-0.182-5.495
> ...
> HB lifetime=50.60ps
> Note that the lifetime obtained in this manner is close to useless.Use the 
> -ac option instead and check the forward lifetime.
> ..
> Will it be correct to say that lifetime is -5.495ps (looking at forward 
> time)? But then what does negative lifetime implies?
> Thanks in advance.

Seems weird. Could the amount of underlying data be insufficient? Have you 
looked at the acf?

Erik

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---
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Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se
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Re: [gmx-users] System exploding

[Justin A. Lemkul]

Lara Bunte wrote:

Hello

If gromacs gives the warning that the system could explode, what could be the 
reason for that?


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

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] System exploding

[Lara Bunte]

Hello

If gromacs gives the warning that the system could explode, what could be the 
reason for that?

Greetings

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Re: [gmx-users] how to optimize hydrogen bonds before simulation?

[Justin A. Lemkul]

Albert wrote:

  Hello:

  I am wondering is it possible to optimize hydrogen bonds network 
before simulation? I've got some crystal solvent in the system and I 
would like to optimize the hbond network even before building a solvent 
system.


Provided the starting configuration does not require large changes, simple 
energy minimization will generally take care of such things.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] how to optimize hydrogen bonds before simulation?

[Albert]

Hello:

  I am wondering is it possible to optimize hydrogen bonds network 
before simulation? I've got some crystal solvent in the system and I 
would like to optimize the hbond network even before building a solvent 
system.


THX
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Re: [gmx-users] About desired Spacing in Distance.pl script

[Justin A. Lemkul]

vidhya sankar wrote:

Dear justin Thank you for your at once reply
  
   I have successfully 
use the Distance.pl I got output. .But in Distance.pl script i have not 
represented the Any  Desired spacing (0.3nm) . Should i Represent? . If  
i need to represent Where Should i represent in Distance .pl script file?
 


I'm not sure what exactly you're asking.  The distance.pl script simply parses 
the g_dist output files to produce a summary that you can inspect to identify 
the coordinate files that can be used later for umbrella sampling.  You decide 
what spacing you need, and by simply reading through the summary_distances.dat 
file, you identify which coordinate files to use.


-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] About desired Spacing in Distance.pl script

[vidhya sankar]

Dear justin Thank you for your at once reply
   

   I have successfully use the 
Distance.pl I got output. .But in Distance.pl script i have not represented the 
Any  Desired spacing (0.3nm) . Should i Represent? . If  i need to represent 
Where Should i represent in Distance .pl script file?-- 
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[gmx-users] How to read in mdcrd files to gromacs?

[a a]

Dear experts,
I am trying to do the following command:
/usr/local/gromacs/bin/g_covar_d -s test.pdb -f test.mdcrd -o -v
But the following error message is found:
---Program g_covar_d, 
VERSION 4.5.5Source code file: trxio.c, line: 870
Fatal error:Not supported in read_first_frame: md0.mdcrdFor more information 
and tips for troubleshooting, please check the GROMACSwebsite at 
http://www.gromacs.org/Documentation/Errors---
What should I do next to solve this problem, I heard GROMACS can read mdcrd 
trajectory files from AMBER, right?
Best regards,
Cat
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[gmx-users] Can GROMACS read binpos trajectory files?

[a a]

Dear Sir,
I am using g_covar version 4.0.7.
I am trying to do:
/share1/gromacs/bin/g_covar -s ../average.pdb -f ../md0.binpos -o -v
However, an error message appear:
 Program g_covar, VERSION 4.0.7Source code file: gmxfio.c, line: 737
Can not open file:../md0.mdcrd.xtc

What should I do next?
Best regards,
Catherine

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Re: [gmx-users] Velocity autocorrelation

[Krzysztof Kuczera]

You probably need to save velocities at least every 10 fs;
look at your plot on a fine enough time scale  - say 0-1 ps range
probably running in NVE ensemble would help as well
Krzysztof Kuczera

On 3/29/12 10:42 AM, Ignacio Fernández Galván wrote:

Dear all,

I'm trying to estimate the correlation time for my system, for the purpose of 
selecting a number of uncorrelated configurations and setting a good value for 
nstxout.

My systems are usually small molecules in molecular liquids (water, methanol, 
acetonitrile, cyclohexane...). As a first approach, I calculate the velocity 
autocorrelation function for the pure liquid (or for a group containing only 
the solvent in a simulation of the full system).

I expect to find a function more or less like the one shown 
here:. But 
instead I get a line that rapidly oscillates around 0, with an amplitude that 
progressively vanishes. I think I understand this behaviour, as it would be due to 
intramolecular vibrations or librations, but I don't find samples of this in the 
literature.

My question is how can analyze this and extract some correlation time? How 
could I get some smooth function like the one shown in the above link? Am I 
doing something wrong? Is there another way to estimate a good value for 
nstxout?

Any help or pointers to where to find it would be appreciated.

Thank you,
Ignacio



--
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Departments of Chemistry and Molecular Biosciences
The University of Kansas
2010 Malott Hall
Lawrence, KS 66045
Tel: 785-864-5060 Fax: 785-864-5396 email: kkucz...@ku.edu
http://oolung.chem.ku.edu/~kuczera/home.html



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[gmx-users] Pressure coupling and Isothermal compressibility for a biphasic system

[bipin singh]

Hello All,

I have some doubts regarding the use of pressure coupling and
isothermal compressibility for a biphasic system (octane+water boxes
built over each other). I have two questions regarding that:

(1) Which pressure coupling (pcoupl) type would be suitable for this
type of system ?

(2) As water and octane have different compressibility, is it possible
to mention the compressibility of water and octane separately?

Please provide your suggestions.



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---
Thanks and Regards,
Bipin Singh
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[gmx-users] HB lifetime

[Nidhi Katyal]

Dear All
I would like to know the strength of the given bond by calculating the
lifetime of that bond.For the same reason i used:
g_hbond -f *.xtc -s *.tpr -ac *.xvg -temp 300 -num *.xvg -life *.xvg
and i got:
TypeRate(1/ps)  Time(ps)  ...
Forward-0.182-5.495
...
HB lifetime=50.60ps
Note that the lifetime obtained in this manner is close to useless.Use the
-ac option instead and check the forward lifetime.
..
Will it be correct to say that lifetime is -5.495ps (looking at forward
time)? But then what does negative lifetime implies?
Thanks in advance.
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Re: [gmx-users] About Distance.pl script

[Justin A. Lemkul]

Dariush Mohammadyani wrote:
I have gotten this error previously. I changed the address of the g_dist 
(e.g. /user/gromacs/bin/g_dist) in distances.pl  
file and it works.
 


Yes, the script assumes the command g_dist exists in your $PATH and is 
unmodified (no prefixes or suffixes).  If this is not the case you will have to 
modify the script so that your executable is called.


-Justin


Dariush

On Thu, Mar 29, 2012 at 11:51 AM, vidhya sankar > wrote:


Dear justin , Thank you for your previous reply
When i Download and  run Distance.pl script In your website I got
the following error


readline() on closed filehandle IN at ./Distance.pl line 16.
Use of uninitialized value $distance in concatenation (.) or string
at ./Distance.pl line 30.

How to rectify this error ?
Thanks in Advance
With regards
S.Vidhyasankar

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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] About Distance.pl script

[Dariush Mohammadyani]

I have gotten this error previously. I changed the address of the g_dist
(e.g. /user/gromacs/bin/g_dist) in distances.pl file and it works.

Dariush

On Thu, Mar 29, 2012 at 11:51 AM, vidhya sankar wrote:

> Dear justin , Thank you for your previous reply
> When i Download and  run Distance.pl script In your website I got the
> following error
>
>
> readline() on closed filehandle IN at ./Distance.pl line 16.
> Use of uninitialized value $distance in concatenation (.) or string at
> ./Distance.pl line 30.
>
> How to rectify this error ?
> Thanks in Advance
> With regards
> S.Vidhyasankar
>
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>
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Re: [gmx-users] About Distance.pl script

[Justin A. Lemkul]

vidhya sankar wrote:

Dear justin , Thank you for your previous reply
When i Download and  run Distance.pl script In your website I got the 
following error



readline() on closed filehandle IN at ./Distance.pl line 16.
Use of uninitialized value $distance in concatenation (.) or string at 
./Distance.pl line 30.


How to rectify this error ?


Those errors will only show up if the g_dist output was not created.  There will 
be other error messages indicating this fact.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Velocity autocorrelation

[Mark Abraham]

On 30/03/2012 2:42 AM, Ignacio Fernández Galván wrote:

Dear all,

I'm trying to estimate the correlation time for my system, for the purpose of 
selecting a number of uncorrelated configurations and setting a good value for 
nstxout.

My systems are usually small molecules in molecular liquids (water, methanol, 
acetonitrile, cyclohexane...). As a first approach, I calculate the velocity 
autocorrelation function for the pure liquid (or for a group containing only 
the solvent in a simulation of the full system).

I expect to find a function more or less like the one shown 
here:. But 
instead I get a line that rapidly oscillates around 0, with an amplitude that 
progressively vanishes. I think I understand this behaviour, as it would be due to 
intramolecular vibrations or librations, but I don't find samples of this in the 
literature.

My question is how can analyze this and extract some correlation time? How 
could I get some smooth function like the one shown in the above link? Am I 
doing something wrong? Is there another way to estimate a good value for 
nstxout?


Manual 3.4.11 and 8.5 has some things to say.

Mark
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Re: [gmx-users] about g_mindist....

[Mark Abraham]

On 30/03/2012 12:40 AM, rama david wrote:

Hi mark ..
thank you for your suggestion..
My command line is g_mindist  -f  ..xtc -s ..tpr -od minimal.xvg  -pi
  protein group contain information about the 284 atom (i.e. All 
protein atoms)


So clearly some part of some molecule is protruding across periodic 
boundaries, since the nearest distance between any periodic image of any 
atom to any original atom is so small. Since your initial structure 
isn't in the square arrangement you think it is in, I suggest you go 
back and set up your system better.


Mark


..
So please suggest  me the right way ..

On Thu, Mar 29, 2012 at 2:02 PM, Mark Abraham > wrote:


On 29/03/2012 7:20 PM, rama david wrote:

Hi everybody ,
I run simulation of 4 same  molecule keep apart in box
of 4 4 4 dimension ..( 71 atom in one molecule = 71 * 4 =
total atom are 284 )
force field = gromacs96   53a6

COM (center of mass) infirmation of molecules
system size :  1.255  1.577  1.883
box vectors :  4.000   4.000   4.000 (nm)
 mol1  : 2.0570.844  1.941
 mol 2  :  2.057  0.844  3.141
 mol 3  : 2.057   3.244   0.744
 mol 4  : 2.057   3.244   3.141

(Four molecule are kept at the four corner of square
 of each side 2.4 nm
   four molecule are catenated in same pdb)


No they're not starting on a square. Look at those z coordinates
above.



 my md.mdp input is like the ..

;Neighborsearching
ns_type= grid; search neighboring grid cells
nstlist= 5; 10 fs
rlist= 1.0; short-range neighborlist cutoff
(in nm)
rcoulomb= 1.0; short-range electrostatic cutoff
(in nm)
rvdw= 1.0; short-range van der Waals cutoff
(in nm)
; Electrostatics
coulombtype= PME; Particle Mesh Ewald for
long-range electrostatics
pme_order= 4; cubic interpolation
fourierspacing= 0.16; grid spacing for FFT

With  command  g_mindist , select option - 1 (Protein )
I got the following result..

The shortest periodic distance is 0.141718 (nm) at time 7692 (ps),
between atoms 26 and 111

Is the simulation is behaving abnormal(I.e  simulation is
wrong ) or  I
 have to select the option system on prompting ??? I am very
new to these simulation field..
so all suggestion are appreciable ...


Shrug. You've measured the inter-group distance between a group
and itself. Curiously enough, that's the length of a C-C bond, or
similar. g_mindist -h is required reading. Also, we don't even
know what's in group Protein, or your g_mindist command line.

Mark
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[gmx-users] About Distance.pl script

[vidhya sankar]

Dear justin , Thank you for your previous reply
When i Download and  run Distance.pl script In your website I got the following 
error


readline() on closed filehandle IN at ./Distance.pl line 16.
Use of uninitialized value $distance in concatenation (.) or string at 
./Distance.pl line 30.

How to rectify this error ?
Thanks in Advance 

With regards
S.Vidhyasankar-- 
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[gmx-users] Velocity autocorrelation

[Ignacio Fernández Galván]

Dear all,

I'm trying to estimate the correlation time for my system, for the purpose of 
selecting a number of uncorrelated configurations and setting a good value for 
nstxout.

My systems are usually small molecules in molecular liquids (water, methanol, 
acetonitrile, cyclohexane...). As a first approach, I calculate the velocity 
autocorrelation function for the pure liquid (or for a group containing only 
the solvent in a simulation of the full system).

I expect to find a function more or less like the one shown here: 
. But instead I 
get a line that rapidly oscillates around 0, with an amplitude that 
progressively vanishes. I think I understand this behaviour, as it would be due 
to intramolecular vibrations or librations, but I don't find samples of this in 
the literature.

My question is how can analyze this and extract some correlation time? How 
could I get some smooth function like the one shown in the above link? Am I 
doing something wrong? Is there another way to estimate a good value for 
nstxout?

Any help or pointers to where to find it would be appreciated.

Thank you,
Ignacio
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Re: [gmx-users] Not able to continue with Equilibration

[Justin A. Lemkul]

francesca vitalini wrote:

My minimization was done without any constraints. I'm starting using
constraints only in the nvt equilibration as I'm trying to equilibrate
my solvent, so, maybe here I'm being extremely naïve, but, shouldn't I
avoid fixing the water in the nvt, as equilibrating it is exactly the
reason I'm running the nvt equilibration? Or am I misunderstanding
something?


You should likely be restraining your protein, not the water.  Bad initial 
geometry (sometimes stuff survives EM) can give your structure a nasty kick that 
causes things to spin out of control.  Restraints on the protein mitigate these 
effects while the water relaxes.


-Justin


Thanks
Francesca



2012/3/29  :

I didn't follow this whole thread, but I sometimes need to turn off all
constraints when doing minimization. In fact, for that reason I entirely
stopped ever using restraints during energy minimization. In extreem cases,
I have had success also by forcing the water to be flexible with a
-DFLEXIBLE (or whatever is appropriate for your water model; check the .itp)
statement in the .mdp file.

Once EM is done, use rigid water and restraints and everything works out ok.

Chris.

-- original message --

Hallo Felix,
thank you for your answer. I tried the constraints = h-bonds but no
change in the output. If I look at the step.pdb file that is produced
after the running I have some strange outcome. For example some of my
atoms are not recognized as part of my protein any more and my
structure is destroied. Am I using some strange parameters for nvt
without realizing it? I've started from the mdp file provided by the
lysozyme tutorial non the Gromacs webpage.
if anyone has any ideas it is more than welcome.
Francesca

integrator  = md; leap-frog integrator
nsteps  = 1 ; 2 * 1 = 20 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 1 ; save coordinates every 0.2 ps
nstvout = 1 ; save velocities every 0.2 ps
nstenergy   = 50; save energies every 0.2 ps
nstlog  = 50; update log file every 0.2 ps
; Bond parameters
unconstrained_start = no
;continuation   = no; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = h-bonds   ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist   = 3.0   ; short-range neighborlist cutoff (in nm)
rcoulomb= 3.0   ; short-range electrostatic cutoff (in nm)
rvdw= 3.0   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = berendsen ; modified Berendsen thermostat
tc-grps = Protein Non-Protein   ; two coupling groups - more
accurate
tau_t   = 0.1 0.1   ; time constant, in ps
ref_t   = 300 300   ; reference temperature, one
for each group, in K
; Pressure coupling is off
pcoupl  = no; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; assign velocities from Maxwell
distribution
gen_temp= 300   ; temperature for Maxwell distribution
gen_seed= -1; generate a random seed



2012/3/29 Rausch, Felix :

[Hide Quoted Text]
Hello again,

Well, I once had problems with simulations crashing randomly during
production runs (sometimes after tens of nanoseconds) with the LINCS
warnings you described. Switching LINCS from "all-bonds" to only "h-bonds"
did the trick for me, although I never exactly figured out why.
Maybe it's worth a try for you, too?
Cheers,
Felix

-Ursprüngliche Nachricht-
Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im
Auftrag von francesca vitalini
Gesendet: Donnerstag, 29. März 2012 15:15
An: Discussion list for GROMACS users
Betreff: Re: [gmx-users] Not able to continue with Equilibration

Hi!
I'm having a similar problem. I have a dimer solvated in a big box of water
plus ions that I have managed to minimize correctly (see output of
minimization at the end) but when I try to run NVT equilibration (see later)
I get LINCS warnings(see below) refearred to atoms which are not in a
cluster or in a strange position. I have added dihedral restraints on them
but still the same type of error. I'm using GROMACS 3.3.1. I have tried to
switch to a newer version of

Re: [gmx-users] Umbrella sampling along Radius of gyration

[felmer...@uchile.cl]

Hey Chris,

 

It is actually not necessary to go to the code. You can do that by compiling a 
version of gromacs including the plumed path for free energy calculations. 
Amogst the several collective variables included there there is gyration radius.

 

Regards

 

Felipe
Mensaje originalDe: chris.neale@utoronto.caFecha: 29-mar-2012 
10:50Para: Asunto: [gmx-users] Umbrella sampling along 
Radius of gyrationIt is not clear to me how one would do this with MD. The only 
thing  that I can think of doing in gromacs is to create a virtual particle  
that is placed at the center of the protein and then apply forces  along the 
vector from this virtual atom to each of the Ca atoms. You  would need to 
modify the gromacs source code so that the Rg was  calculated at each step and 
the magnitude of each force is scaled  appropriately such that you get a 
harmonic potential about the desired  value of Rg. It should be easier to do 
with MC (although that's a ways  off for gromacs unless I've missed 
something).Some people appear to have done exactly what you want with MD. I  
presume that they used charmm.http://www.pnas.org/content/94/19/10161.long (and 
their reference 22).Chris.-- original message --Hi,   Is there any way in 
gromacs to use radius of gyration of a polymer  as reaction coordinate for 
umbrella sampling ?ThanksSanku-- gmx-users mailing list
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Re: [gmx-users] Not able to continue with Equilibration

[francesca vitalini]

My minimization was done without any constraints. I'm starting using
constraints only in the nvt equilibration as I'm trying to equilibrate
my solvent, so, maybe here I'm being extremely naïve, but, shouldn't I
avoid fixing the water in the nvt, as equilibrating it is exactly the
reason I'm running the nvt equilibration? Or am I misunderstanding
something?
Thanks
Francesca



2012/3/29  :
> I didn't follow this whole thread, but I sometimes need to turn off all
> constraints when doing minimization. In fact, for that reason I entirely
> stopped ever using restraints during energy minimization. In extreem cases,
> I have had success also by forcing the water to be flexible with a
> -DFLEXIBLE (or whatever is appropriate for your water model; check the .itp)
> statement in the .mdp file.
>
> Once EM is done, use rigid water and restraints and everything works out ok.
>
> Chris.
>
> -- original message --
>
> Hallo Felix,
> thank you for your answer. I tried the constraints = h-bonds but no
> change in the output. If I look at the step.pdb file that is produced
> after the running I have some strange outcome. For example some of my
> atoms are not recognized as part of my protein any more and my
> structure is destroied. Am I using some strange parameters for nvt
> without realizing it? I've started from the mdp file provided by the
> lysozyme tutorial non the Gromacs webpage.
> if anyone has any ideas it is more than welcome.
> Francesca
>
> integrator      = md            ; leap-frog integrator
> nsteps          = 1         ; 2 * 1 = 20 ps
> dt              = 0.002         ; 2 fs
> ; Output control
> nstxout         = 1             ; save coordinates every 0.2 ps
> nstvout         = 1             ; save velocities every 0.2 ps
> nstenergy       = 50            ; save energies every 0.2 ps
> nstlog          = 50            ; update log file every 0.2 ps
> ; Bond parameters
> unconstrained_start = no
> ;continuation   = no            ; first dynamics run
> constraint_algorithm = lincs    ; holonomic constraints
> constraints     = h-bonds       ; all bonds (even heavy atom-H bonds)
> constrained
> lincs_iter      = 1             ; accuracy of LINCS
> lincs_order     = 4             ; also related to accuracy
> ; Neighborsearching
> ns_type         = grid          ; search neighboring grid cells
> nstlist         = 5             ; 10 fs
> rlist           = 3.0           ; short-range neighborlist cutoff (in nm)
> rcoulomb        = 3.0           ; short-range electrostatic cutoff (in nm)
> rvdw            = 3.0           ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype     = PME           ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order       = 4             ; cubic interpolation
> fourierspacing  = 0.16          ; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl          = berendsen     ; modified Berendsen thermostat
> tc-grps         = Protein Non-Protein   ; two coupling groups - more
> accurate
> tau_t           = 0.1 0.1       ; time constant, in ps
> ref_t           = 300 300               ; reference temperature, one
> for each group, in K
> ; Pressure coupling is off
> pcoupl          = no            ; no pressure coupling in NVT
> ; Periodic boundary conditions
> pbc             = xyz           ; 3-D PBC
> ; Dispersion correction
> DispCorr        = EnerPres      ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel         = yes           ; assign velocities from Maxwell
> distribution
> gen_temp        = 300           ; temperature for Maxwell distribution
> gen_seed        = -1            ; generate a random seed
>
>
>
> 2012/3/29 Rausch, Felix :
>
> [Hide Quoted Text]
> Hello again,
>
> Well, I once had problems with simulations crashing randomly during
> production runs (sometimes after tens of nanoseconds) with the LINCS
> warnings you described. Switching LINCS from "all-bonds" to only "h-bonds"
> did the trick for me, although I never exactly figured out why.
> Maybe it's worth a try for you, too?
> Cheers,
> Felix
>
> -Ursprüngliche Nachricht-
> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im
> Auftrag von francesca vitalini
> Gesendet: Donnerstag, 29. März 2012 15:15
> An: Discussion list for GROMACS users
> Betreff: Re: [gmx-users] Not able to continue with Equilibration
>
> Hi!
> I'm having a similar problem. I have a dimer solvated in a big box of water
> plus ions that I have managed to minimize correctly (see output of
> minimization at the end) but when I try to run NVT equilibration (see later)
> I get LINCS warnings(see below) refearred to atoms which are not in a
> cluster or in a strange position. I have added dihedral restraints on them
> but still the same type of error. I'm using GROMACS 3.3.1. I have tried to
> switch to a newer version of GROMACS but still the same error.
> Does anyone have any suggestions?
> Thanks
> Francesca
>
>
> MINIMIZATION OUTPUT
>
> Steepes

Re: [gmx-users] Not able to continue with Equilibration

[Justin A. Lemkul]

francesca vitalini wrote:

Hallo Felix,
thank you for your answer. I tried the constraints = h-bonds but no
change in the output. If I look at the step.pdb file that is produced
after the running I have some strange outcome. For example some of my
atoms are not recognized as part of my protein any more and my
structure is destroied. Am I using some strange parameters for nvt
without realizing it? I've started from the mdp file provided by the
lysozyme tutorial non the Gromacs webpage.


Yes, some of your parameters are very strange:


rlist   = 3.0   ; short-range neighborlist cutoff (in nm)
rcoulomb= 3.0   ; short-range electrostatic cutoff (in nm)
rvdw= 3.0   ; short-range van der Waals cutoff (in nm)


None of the force fields in Gromacs are parameterized to use such values.  Your 
crash could be due to the fact that you're breaking the underlying physics.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Not able to continue with Equilibration

[chris . neale]

I didn't follow this whole thread, but I sometimes need to turn off  
all constraints when doing minimization. In fact, for that reason I  
entirely stopped ever using restraints during energy minimization. In  
extreem cases, I have had success also by forcing the water to be  
flexible with a -DFLEXIBLE (or whatever is appropriate for your water  
model; check the .itp) statement in the .mdp file.


Once EM is done, use rigid water and restraints and everything works out ok.

Chris.

-- original message --

Hallo Felix,
thank you for your answer. I tried the constraints = h-bonds but no
change in the output. If I look at the step.pdb file that is produced
after the running I have some strange outcome. For example some of my
atoms are not recognized as part of my protein any more and my
structure is destroied. Am I using some strange parameters for nvt
without realizing it? I've started from the mdp file provided by the
lysozyme tutorial non the Gromacs webpage.
if anyone has any ideas it is more than welcome.
Francesca

integrator  = md; leap-frog integrator
nsteps  = 1 ; 2 * 1 = 20 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 1 ; save coordinates every 0.2 ps
nstvout = 1 ; save velocities every 0.2 ps
nstenergy   = 50; save energies every 0.2 ps
nstlog  = 50; update log file every 0.2 ps
; Bond parameters
unconstrained_start = no
;continuation   = no; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = h-bonds   ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist   = 3.0   ; short-range neighborlist cutoff (in nm)
rcoulomb= 3.0   ; short-range electrostatic cutoff (in nm)
rvdw= 3.0   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = berendsen ; modified Berendsen thermostat
tc-grps = Protein Non-Protein   ; two coupling groups - more accurate
tau_t   = 0.1 0.1   ; time constant, in ps
ref_t   = 300 300   ; reference temperature, one
for each group, in K
; Pressure coupling is off
pcoupl  = no; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; assign velocities from Maxwell distribution
gen_temp= 300   ; temperature for Maxwell distribution
gen_seed= -1; generate a random seed



2012/3/29 Rausch, Felix :

[Hide Quoted Text]
Hello again,

Well, I once had problems with simulations crashing randomly during  
production runs (sometimes after tens of nanoseconds) with the LINCS  
warnings you described. Switching LINCS from "all-bonds" to only  
"h-bonds" did the trick for me, although I never exactly figured out  
why.

Maybe it's worth a try for you, too?
Cheers,
Felix

-Ursprüngliche Nachricht-
Von: gmx-users-boun...@gromacs.org  
[mailto:gmx-users-boun...@gromacs.org] Im Auftrag von francesca vitalini

Gesendet: Donnerstag, 29. März 2012 15:15
An: Discussion list for GROMACS users
Betreff: Re: [gmx-users] Not able to continue with Equilibration

Hi!
I'm having a similar problem. I have a dimer solvated in a big box of  
water plus ions that I have managed to minimize correctly (see output  
of minimization at the end) but when I try to run NVT equilibration  
(see later) I get LINCS warnings(see below) refearred to atoms which  
are not in a cluster or in a strange position. I have added dihedral  
restraints on them but still the same type of error. I'm using GROMACS  
3.3.1. I have tried to switch to a newer version of GROMACS but still  
the same error.

Does anyone have any suggestions?
Thanks
Francesca


MINIMIZATION OUTPUT

Steepest Descents converged to Fmax < 1000 in 681 steps Potential  
Energy  = -1.9597512e+07

Maximum force =  2.4159846e+02 on atom 13087
Norm of force =  2.1520395e+04


MINIMIZATION.MDP

define = -DEFLEXIBLE ; flexible water
integrator  = steep ; Algorithm (steep = steepest descent
minimization)
emtol   = 1000.0 ; Stop minimization when the maximum
force < 1000.0 kJ/mol/nm
emstep  = 0.001  ; Energy step size
nsteps  = 5 ; Maximum number of (minimization)
steps to perform

; 

Re: [gmx-users] Not able to continue with Equilibration

[francesca vitalini]

Hallo Felix,
thank you for your answer. I tried the constraints = h-bonds but no
change in the output. If I look at the step.pdb file that is produced
after the running I have some strange outcome. For example some of my
atoms are not recognized as part of my protein any more and my
structure is destroied. Am I using some strange parameters for nvt
without realizing it? I've started from the mdp file provided by the
lysozyme tutorial non the Gromacs webpage.
if anyone has any ideas it is more than welcome.
Francesca

integrator  = md; leap-frog integrator
nsteps  = 1 ; 2 * 1 = 20 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 1 ; save coordinates every 0.2 ps
nstvout = 1 ; save velocities every 0.2 ps
nstenergy   = 50; save energies every 0.2 ps
nstlog  = 50; update log file every 0.2 ps
; Bond parameters
unconstrained_start = no
;continuation   = no; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = h-bonds   ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist   = 3.0   ; short-range neighborlist cutoff (in nm)
rcoulomb= 3.0   ; short-range electrostatic cutoff (in nm)
rvdw= 3.0   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = berendsen ; modified Berendsen thermostat
tc-grps = Protein Non-Protein   ; two coupling groups - more accurate
tau_t   = 0.1 0.1   ; time constant, in ps
ref_t   = 300 300   ; reference temperature, one
for each group, in K
; Pressure coupling is off
pcoupl  = no; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; assign velocities from Maxwell distribution
gen_temp= 300   ; temperature for Maxwell distribution
gen_seed= -1; generate a random seed



2012/3/29 Rausch, Felix :
> Hello again,
>
> Well, I once had problems with simulations crashing randomly during 
> production runs (sometimes after tens of nanoseconds) with the LINCS warnings 
> you described. Switching LINCS from "all-bonds" to only "h-bonds" did the 
> trick for me, although I never exactly figured out why.
> Maybe it's worth a try for you, too?
> Cheers,
> Felix
>
> -Ursprüngliche Nachricht-
> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im 
> Auftrag von francesca vitalini
> Gesendet: Donnerstag, 29. März 2012 15:15
> An: Discussion list for GROMACS users
> Betreff: Re: [gmx-users] Not able to continue with Equilibration
>
> Hi!
> I'm having a similar problem. I have a dimer solvated in a big box of water 
> plus ions that I have managed to minimize correctly (see output of 
> minimization at the end) but when I try to run NVT equilibration (see later) 
> I get LINCS warnings(see below) refearred to atoms which are not in a cluster 
> or in a strange position. I have added dihedral restraints on them but still 
> the same type of error. I'm using GROMACS 3.3.1. I have tried to switch to a 
> newer version of GROMACS but still the same error.
> Does anyone have any suggestions?
> Thanks
> Francesca
>
>
> MINIMIZATION OUTPUT
>
> Steepest Descents converged to Fmax < 1000 in 681 steps Potential Energy  = 
> -1.9597512e+07
> Maximum force     =  2.4159846e+02 on atom 13087
> Norm of force     =  2.1520395e+04
>
>
> MINIMIZATION.MDP
>
> define         = -DEFLEXIBLE ; flexible water
> integrator      = steep         ; Algorithm (steep = steepest descent
> minimization)
> emtol           = 1000.0         ; Stop minimization when the maximum
> force < 1000.0 kJ/mol/nm
> emstep          = 0.001          ; Energy step size
> nsteps          = 5         ; Maximum number of (minimization)
> steps to perform
>
> ; 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
> 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 interacti

[gmx-users] Umbrella sampling along Radius of gyration

[chris . neale]

It is not clear to me how one would do this with MD. The only thing  
that I can think of doing in gromacs is to create a virtual particle  
that is placed at the center of the protein and then apply forces  
along the vector from this virtual atom to each of the Ca atoms. You  
would need to modify the gromacs source code so that the Rg was  
calculated at each step and the magnitude of each force is scaled  
appropriately such that you get a harmonic potential about the desired  
value of Rg. It should be easier to do with MC (although that's a ways  
off for gromacs unless I've missed something).


Some people appear to have done exactly what you want with MD. I  
presume that they used charmm.


http://www.pnas.org/content/94/19/10161.long (and their reference 22).

Chris.

-- original message --

Hi,
  Is there any way in gromacs to use radius of gyration of a polymer  
as reaction coordinate for umbrella sampling ?

Thanks
Sanku



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AW: [gmx-users] Not able to continue with Equilibration

[Rausch, Felix]

Hello again,

Well, I once had problems with simulations crashing randomly during production 
runs (sometimes after tens of nanoseconds) with the LINCS warnings you 
described. Switching LINCS from "all-bonds" to only "h-bonds" did the trick for 
me, although I never exactly figured out why. 
Maybe it's worth a try for you, too?
Cheers,
Felix

-Ursprüngliche Nachricht-
Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im 
Auftrag von francesca vitalini
Gesendet: Donnerstag, 29. März 2012 15:15
An: Discussion list for GROMACS users
Betreff: Re: [gmx-users] Not able to continue with Equilibration

Hi!
I'm having a similar problem. I have a dimer solvated in a big box of water 
plus ions that I have managed to minimize correctly (see output of minimization 
at the end) but when I try to run NVT equilibration (see later) I get LINCS 
warnings(see below) refearred to atoms which are not in a cluster or in a 
strange position. I have added dihedral restraints on them but still the same 
type of error. I'm using GROMACS 3.3.1. I have tried to switch to a newer 
version of GROMACS but still the same error.
Does anyone have any suggestions?
Thanks
Francesca


MINIMIZATION OUTPUT

Steepest Descents converged to Fmax < 1000 in 681 steps Potential Energy  = 
-1.9597512e+07
Maximum force =  2.4159846e+02 on atom 13087
Norm of force =  2.1520395e+04


MINIMIZATION.MDP

define = -DEFLEXIBLE ; flexible water
integrator  = steep ; Algorithm (steep = steepest descent
minimization)
emtol   = 1000.0 ; Stop minimization when the maximum
force < 1000.0 kJ/mol/nm
emstep  = 0.001  ; Energy step size
nsteps  = 5 ; Maximum number of (minimization)
steps to perform

; 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
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   ; Short-range electrostatic cut-off
rvdw= 1.0   ; Short-range Van der Waals cut-off
pbc = xyz   ; Periodic Boundary Conditions (yes/no)


NVT.MDP

define  = -DPOSRES  ; position restrain the protein
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 1 ; 2 * 1 = 20 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 50; save coordinates every 0.2 ps
nstvout = 50; save velocities every 0.2 ps
nstenergy   = 50; save energies every 0.2 ps
nstlog  = 50; update log file every 0.2 ps
; Bond parameters
unconstrained_start = no
;continuation   = no; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist   = 3.0   ; short-range neighborlist cutoff (in nm)
rcoulomb= 3.0   ; short-range electrostatic cutoff (in nm)
rvdw= 3.0   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = berendsen ; modified Berendsen thermostat
tc-grps = Protein Non-Protein   ; two coupling groups - more accurate
tau_t   = 0.1 0.1   ; time constant, in ps
ref_t   = 300 300   ; reference temperature, one
for each group, in K
; Pressure coupling is off
pcoupl  = no; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; assign velocities from Maxwell distribution
gen_temp= 300   ; temperature for Maxwell distribution
gen_seed= -1; generate a random seed

; Dihedral restraints

dihre   =  simple ; Some dihedrals are restrained  for
instance peptide bonds are set to trans conformation.
dihre_fc=  500
dihre_tau   =  0.0
nstdihreout =  50

NVT LINCS ERROR

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.002851 (between atoms 10721 

Re: [gmx-users] How to fix Water during simulation ?

[Justin A. Lemkul]

ajani haresh wrote:

Hello Everyone,

I am new in Gromacs. I am using gromacs for protein-ligand complex.

I have few question  ?

1): how to fix water during simulation ?



If pdb2gmx wrote the topology, you should be able to invoke "define = 
-DPOSRES_WATER" in the .mdp file.  Check your topology (after the #include 
statement for water) to be sure.



2): how to fix protein and ligand during simulation ?



With position restraints.  They will need their own posre.itp files, unless you 
have merged the [moleculetypes], in which case a single posre.itp file is needed.



3) how to fix few crystal water molecule during simulation  ?

4) how to fix specific water molecule  in simulation ?




Restraining groups of water is tricky.  Position restraints can only be applied 
to individual [moleculetype] directives, so whatever you restrain has to be 
defined as such.  The problem then becomes that you cannot have separate blocks 
of water molecules using the SETTLE algorithm for their constraints.  The same 
problem applies if you using freezegrps in the .mdp file.  You can get around 
this by hacking the topology to include normal constraints for each water 
molecule you're trying to work with.  That becomes a huge pain and will likely 
make you question whether you need to go to all this trouble ;)


Note that freezing and restraining are separate concepts (see the manual and 
webpage).


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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Re: [gmx-users] About cutt-off scheme ..

[Justin A. Lemkul]

rama david wrote:

Hi justin,
 thank you for reply,
1.I sort out the specific time pdb ..
 I notice the folllowing things.. 
 26 and 111 are the atoms of two different protein ..
 one is  on the right hand side near the box boundary ..and other is 
protruding from the 
 left hand side box boundary ,so they may close to each other enough ..

 so is the simulation is wrong or right ...



This seems fine.  The point of the minimum image convention is that one should 
not allow the same molecule to double-count interactions due to periodicity. 
Two different molecules interacting is not a big deal, that's just what happens 
across PBC.


If you have 4 proteins, each at the "corner" of the box (which is irrelevant due 
to PBC), it's the same as having all four clustered in the "center" of the box 
to begin with.  Use a periodic representation in VMD (or whatever you like) to 
see what I mean.


2.   Please could you tell me , What are the right parameter for the G96 
53a6 force field ??




With PME, you would use:

rlist = 0.9
rcoulomb = 0.9
rvdw = 1.4

-Justin


thank you a lot for help ..

On Thu, Mar 29, 2012 at 7:03 PM, rama david > wrote:


Hi Gromacs friends,
  Thank you justin for your explaination ..

It is, however, common to compromise
in this respect, and make the solvent layer somewhat smaller in
order to reduce the computational
cost. For efficiency reasons the cut-off with triclinic boxes is
more restricted. For grid search the
extra restriction is weak:

Rc < min(ax; by; cz) (3.5)

For simple search the extra restriction is stronger:

Rc <1/2min(ax; by; cz) (3.6)   


So from manual and your answer , should I conclude that -d 1.0 nm
distance is sufficient  ???

if I using command genbox . -ci  -nmol ... , the molecule are
going to put randomly ..
In that case how to maintain  -d  .. ??? 
I am in these confusion because of following reason . 


I am try to put max molecule to study there interaction ...

 I run simulation of 4 same  molecule keep apart in box  
of 4 4 4 dimension ..( 71 atom in one molecule = 71 * 4 = total atom

are 284 )
force field = gromacs96   53a6

COM (center of mass) information of molecules
system size :  1.255  1.577  1.883 
box vectors :  4.000   4.000   4.000 (nm)

 mol1  : 2.0570.844  0.744
 mol 2  :  2.057  0.844  3.141
 mol 3  : 2.057   3.244   0.744
 mol 4  : 2.057   3.244   3.141

(Four molecule are kept at the four corner of square
 of each side 2.4 nm
four molecule are catenated in same pdb)

 my md.mdp input is like the ..

;Neighborsearching
ns_type= grid; search neighboring grid cells
nstlist= 5; 10 fs
rlist= 1.0; short-range neighborlist cutoff (in nm)
rcoulomb= 1.0; short-range electrostatic cutoff (in nm)
rvdw= 1.0; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype= PME; Particle Mesh Ewald for long-range
electrostatics
pme_order= 4; cubic interpolation
fourierspacing= 0.16; grid spacing for FFT

With  command  g_mindist-pi 
 , select option - 1 (Protein )

In the index file protein contain information on protein ...
I got the following result.. 


The shortest periodic distance is 0.141718 (nm) at time 7692 (ps),
between atoms 26 and 111

Is the simulation is behaving abnormal(I.e  simulation is wrong ) or  I
 have to select the option system on prompting ??? I am very new to
these simulation field.. 
so all suggestion are appreciable ...


   


On Thu, Mar 29, 2012 at 5:05 PM, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote:



rama david wrote:

Hi Gromacs users ,
as per the link given on gromacs website...
Introduction to Molecular Dynamics Simulations and Analysis
> - Tutorial
for performing and analyzing simulations of proteins.
Includes examples of many of the gromacs analysis tools and
addresses a number of issues that are commonly raised on the
GROMACS user list. This tutorial uses GROMACS version 3.3.1
(Tsjerk A. Wassenaar).



editconf -f protein-EM-vacuum.pdb -o protein-PBC.gro -bt
dodecahedron -d 1.0

mdp file parameter are as follow ,

coulombtype  = Reaction-Field
rcoulomb = 1.4
epsilon_rf   = 78
epsilon_r= 1
vdw-type = Cut-off
rvdw  

[gmx-users] How to fix Water during simulation ?

[ajani haresh]

Hello Everyone,

I am new in Gromacs. I am using gromacs for protein-ligand complex.

I have few question  ?

1): how to fix water during simulation ?

2): how to fix protein and ligand during simulation ?

3) how to fix few crystal water molecule during simulation  ?

4) how to fix specific water molecule  in simulation ?



Thanks in advance.


-- 
-
Haresh Ajani
09925522578
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Re: [gmx-users] About cutt-off scheme ..

[rama david]

Hi justin,
 thank you for reply,
1.I sort out the specific time pdb ..
 I notice the folllowing things..
 26 and 111 are the atoms of two different protein ..
 one is  on the right hand side near the box boundary ..and other is
protruding from the
 left hand side box boundary ,so they may close to each other enough ..
 so is the simulation is wrong or right ...

2.   Please could you tell me , What are the right parameter for the G96
53a6 force field ??

thank you a lot for help ..

On Thu, Mar 29, 2012 at 7:03 PM, rama david wrote:

> Hi Gromacs friends,
>   Thank you justin for your explaination ..
>
> It is, however, common to compromise
> in this respect, and make the solvent layer somewhat smaller in order to
> reduce the computational
> cost. For efficiency reasons the cut-off with triclinic boxes is more
> restricted. For grid search the
> extra restriction is weak:
>
> Rc < min(ax; by; cz) (3.5)
>
> For simple search the extra restriction is stronger:
>
> Rc <1/2min(ax; by; cz) (3.6)
>
> So from manual and your answer , should I conclude that -d 1.0 nm distance
> is sufficient  ???
>
> if I using command genbox . -ci  -nmol ... , the molecule are going to
> put randomly ..
> In that case how to maintain  -d  .. ???
> I am in these confusion because of following reason .
>
> I am try to put max molecule to study there interaction ...
>
>  I run simulation of 4 same  molecule keep apart in box
> of 4 4 4 dimension ..( 71 atom in one molecule = 71 * 4 = total atom are
> 284 )
> force field = gromacs96   53a6
>
> COM (center of mass) information of molecules
> system size :  1.255  1.577  1.883
> box vectors :  4.000   4.000   4.000 (nm)
>  mol1  : 2.0570.844  0.744
>  mol 2  :  2.057  0.844  3.141
>  mol 3  : 2.057   3.244   0.744
>  mol 4  : 2.057   3.244   3.141
>
> (Four molecule are kept at the four corner of square
>  of each side 2.4 nm
> four molecule are catenated in same pdb)
>
>  my md.mdp input is like the ..
>
> ;Neighborsearching
> ns_type= grid; search neighboring grid cells
> nstlist= 5; 10 fs
> rlist= 1.0; short-range neighborlist cutoff (in nm)
> rcoulomb= 1.0; short-range electrostatic cutoff (in nm)
> rvdw= 1.0; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype= PME; Particle Mesh Ewald for long-range
> electrostatics
> pme_order= 4; cubic interpolation
> fourierspacing= 0.16; grid spacing for FFT
>
> With  command  g_mindist-pi
>  , select option - 1 (Protein )
> In the index file protein contain information on protein ...
> I got the following result..
>
> The shortest periodic distance is 0.141718 (nm) at time 7692 (ps),
> between atoms 26 and 111
>
> Is the simulation is behaving abnormal(I.e  simulation is wrong ) or  I
>  have to select the option system on prompting ??? I am very new to these
> simulation field..
> so all suggestion are appreciable ...
>
>
>
> On Thu, Mar 29, 2012 at 5:05 PM, Justin A. Lemkul  wrote:
>
>>
>>
>> rama david wrote:
>>
>>> Hi Gromacs users ,
>>> as per the link given on gromacs website...
>>> Introduction to Molecular Dynamics Simulations and Analysis <
>>> http://nmr.chem.uu.nl/%**7Etsjerk/course/molmod/>
>>> - Tutorial for performing and analyzing simulations of proteins. Includes
>>> examples of many of the gromacs analysis tools and addresses a number of
>>> issues that are commonly raised on the GROMACS user list. This tutorial
>>> uses GROMACS version 3.3.1 (Tsjerk A. Wassenaar).
>>>
>>>
>>>
>>> editconf -f protein-EM-vacuum.pdb -o protein-PBC.gro -bt dodecahedron -d
>>> 1.0
>>>
>>> mdp file parameter are as follow ,
>>>
>>> coulombtype  = Reaction-Field
>>> rcoulomb = 1.4
>>> epsilon_rf   = 78
>>> epsilon_r= 1
>>> vdw-type = Cut-off
>>> rvdw = 1.4
>>>  so my query  is ..
>>>
>>> As mention in manual ...
>>> (Page no 14  manual 4.5.4  I am using the Gromacs 4.5.4  )
>>> *This means that the length of each box vector must exceed the length of
>>> the macromolecule in the
>>> direction of that edge plus two times the cut-off radius Rc *.
>>>
>>
>> Read the next sentence in the manual.
>>
>> /In  the tutorial  -d 1.0  is less than 1.4  ./..
>>>
>>>  I noticed that manual version and tutorial  gromacs version are
>>> different ...
>>> But it raise a lot of confusion  for new users like me..
>>>  1. Is the -d .. should be equal  or more than cutt off ???
>>> or
>>>  Is the -d   .. should be equal or more than cutt-off??
>>>
>>>
>> The basic point is that in all simulations you have to avoid the same
>> molecule "seeing" itself across a periodic boundary.  So in reality, you
>> need a periodic distance (which is equivalent to the value set with -d,
>> times 2) that 

Re: [gmx-users] About cutt-off scheme ..

[Justin A. Lemkul]

rama david wrote:

Hi Gromacs friends,
  Thank you justin for your explaination ..

It is, however, common to compromise
in this respect, and make the solvent layer somewhat smaller in order to 
reduce the computational
cost. For efficiency reasons the cut-off with triclinic boxes is more 
restricted. For grid search the

extra restriction is weak:

Rc < min(ax; by; cz) (3.5)

For simple search the extra restriction is stronger:

Rc <1/2min(ax; by; cz) (3.6)   

So from manual and your answer , should I conclude that -d 1.0 nm 
distance is sufficient  ???


if I using command genbox . -ci  -nmol ... , the molecule are going 
to put randomly ..
In that case how to maintain  -d  .. ??? 
I am in these confusion because of following reason . 


I am try to put max molecule to study there interaction ...

 I run simulation of 4 same  molecule keep apart in box  
of 4 4 4 dimension ..( 71 atom in one molecule = 71 * 4 = total atom are 
284 )

force field = gromacs96   53a6

COM (center of mass) information of molecules
system size :  1.255  1.577  1.883 
box vectors :  4.000   4.000   4.000 (nm)

 mol1  : 2.0570.844  0.744
 mol 2  :  2.057  0.844  3.141
 mol 3  : 2.057   3.244   0.744
 mol 4  : 2.057   3.244   3.141

(Four molecule are kept at the four corner of square
 of each side 2.4 nm
four molecule are catenated in same pdb)

 my md.mdp input is like the ..

;Neighborsearching
ns_type= grid; search neighboring grid cells
nstlist= 5; 10 fs
rlist= 1.0; short-range neighborlist cutoff (in nm)
rcoulomb= 1.0; short-range electrostatic cutoff (in nm)
rvdw= 1.0; short-range van der Waals cutoff (in nm)


These settings are not correct for Gromos96 53a6.


; Electrostatics
coulombtype= PME; Particle Mesh Ewald for long-range 
electrostatics

pme_order= 4; cubic interpolation
fourierspacing= 0.16; grid spacing for FFT

With  command  g_mindist-pi 
 , select option - 1 (Protein )

In the index file protein contain information on protein ...
I got the following result.. 


The shortest periodic distance is 0.141718 (nm) at time 7692 (ps),
between atoms 26 and 111



Identify what atoms 26 and 111 are.  If they are part of the same molecule, then 
yes, you have a problem.  It sounds to me like you have 4 separate molecules, 
and 2 of them are at a very short distance in the starting configuration.  This 
is not the same situation as when a molecule sees itself.  Whether or not this 
is what you want for your simulation setup is up to you.


-Justin


Is the simulation is behaving abnormal(I.e  simulation is wrong ) or  I
 have to select the option system on prompting ??? I am very new to 
these simulation field.. 
so all suggestion are appreciable ...


   

On Thu, Mar 29, 2012 at 5:05 PM, Justin A. Lemkul > wrote:




rama david wrote:

Hi Gromacs users ,
as per the link given on gromacs website...
Introduction to Molecular Dynamics Simulations and Analysis
> - Tutorial for
performing and analyzing simulations of proteins. Includes
examples of many of the gromacs analysis tools and addresses a
number of issues that are commonly raised on the GROMACS user
list. This tutorial uses GROMACS version 3.3.1 (Tsjerk A.
Wassenaar).



editconf -f protein-EM-vacuum.pdb -o protein-PBC.gro -bt
dodecahedron -d 1.0

mdp file parameter are as follow ,

coulombtype  = Reaction-Field
rcoulomb = 1.4
epsilon_rf   = 78
epsilon_r= 1
vdw-type = Cut-off
rvdw = 1.4
 so my query  is ..

As mention in manual ...
(Page no 14  manual 4.5.4  I am using the Gromacs 4.5.4  )
*This means that the length of each box vector must exceed the
length of the macromolecule in the
direction of that edge plus two times the cut-off radius Rc *.


Read the next sentence in the manual.

   /In  the tutorial  -d 1.0  is less than 1.4  ./..

 I noticed that manual version and tutorial  gromacs version are
different ...
But it raise a lot of confusion  for new users like me..
 1. Is the -d .. should be equal  or more than cutt off ???
or
 Is the -d   .. should be equal or more than cutt-off??


The basic point is that in all simulations you have to avoid the
same molecule "seeing" itself across a periodic boundary.  So in
reality, you need a periodic distance (which is equivalent to the
value set with -d, times 2) that exceeds the longest cutoff.
 Assuming the unit cell does not u

Re: [gmx-users] about g_mindist....

[rama david]

Hi mark ..
thank you for your suggestion..
My command line is g_mindist  -f  ..xtc -s ..tpr -od minimal.xvg  -pi
  protein group contain information about the 284 atom (i.e. All protein
atoms)
..
So please suggest  me the right way ..

On Thu, Mar 29, 2012 at 2:02 PM, Mark Abraham wrote:

> On 29/03/2012 7:20 PM, rama david wrote:
>
>> Hi everybody ,
>> I run simulation of 4 same  molecule keep apart in box
>> of 4 4 4 dimension ..( 71 atom in one molecule = 71 * 4 = total atom are
>> 284 )
>> force field = gromacs96   53a6
>>
>> COM (center of mass) infirmation of molecules
>> system size :  1.255  1.577  1.883
>> box vectors :  4.000   4.000   4.000 (nm)
>>  mol1  : 2.0570.844  1.941
>>  mol 2  :  2.057  0.844  3.141
>>  mol 3  : 2.057   3.244   0.744
>>  mol 4  : 2.057   3.244   3.141
>>
>> (Four molecule are kept at the four corner of square
>>  of each side 2.4 nm
>>four molecule are catenated in same pdb)
>>
>
> No they're not starting on a square. Look at those z coordinates above.
>
>
>
>>  my md.mdp input is like the ..
>>
>> ;Neighborsearching
>> ns_type= grid; search neighboring grid cells
>> nstlist= 5; 10 fs
>> rlist= 1.0; short-range neighborlist cutoff (in nm)
>> rcoulomb= 1.0; short-range electrostatic cutoff (in nm)
>> rvdw= 1.0; short-range van der Waals cutoff (in nm)
>> ; Electrostatics
>> coulombtype= PME; Particle Mesh Ewald for long-range
>> electrostatics
>> pme_order= 4; cubic interpolation
>> fourierspacing= 0.16; grid spacing for FFT
>>
>> With  command  g_mindist , select option - 1 (Protein )
>> I got the following result..
>>
>> The shortest periodic distance is 0.141718 (nm) at time 7692 (ps),
>> between atoms 26 and 111
>>
>> Is the simulation is behaving abnormal(I.e  simulation is wrong ) or  I
>>  have to select the option system on prompting ??? I am very new to these
>> simulation field..
>> so all suggestion are appreciable ...
>>
>
> Shrug. You've measured the inter-group distance between a group and
> itself. Curiously enough, that's the length of a C-C bond, or similar.
> g_mindist -h is required reading. Also, we don't even know what's in group
> Protein, or your g_mindist command line.
>
> Mark
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  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/**Support/Mailing_Lists
>
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Re: [gmx-users] About cutt-off scheme ..

[rama david]

Hi Gromacs friends,
  Thank you justin for your explaination ..

It is, however, common to compromise
in this respect, and make the solvent layer somewhat smaller in order to
reduce the computational
cost. For efficiency reasons the cut-off with triclinic boxes is more
restricted. For grid search the
extra restriction is weak:

Rc < min(ax; by; cz) (3.5)

For simple search the extra restriction is stronger:

Rc <1/2min(ax; by; cz) (3.6)

So from manual and your answer , should I conclude that -d 1.0 nm distance
is sufficient  ???

if I using command genbox . -ci  -nmol ... , the molecule are going to
put randomly ..
In that case how to maintain  -d  .. ???
I am in these confusion because of following reason .

I am try to put max molecule to study there interaction ...

 I run simulation of 4 same  molecule keep apart in box
of 4 4 4 dimension ..( 71 atom in one molecule = 71 * 4 = total atom are
284 )
force field = gromacs96   53a6

COM (center of mass) information of molecules
system size :  1.255  1.577  1.883
box vectors :  4.000   4.000   4.000 (nm)
 mol1  : 2.0570.844  0.744
 mol 2  :  2.057  0.844  3.141
 mol 3  : 2.057   3.244   0.744
 mol 4  : 2.057   3.244   3.141

(Four molecule are kept at the four corner of square
 of each side 2.4 nm
four molecule are catenated in same pdb)

 my md.mdp input is like the ..

;Neighborsearching
ns_type= grid; search neighboring grid cells
nstlist= 5; 10 fs
rlist= 1.0; short-range neighborlist cutoff (in nm)
rcoulomb= 1.0; short-range electrostatic cutoff (in nm)
rvdw= 1.0; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype= PME; Particle Mesh Ewald for long-range
electrostatics
pme_order= 4; cubic interpolation
fourierspacing= 0.16; grid spacing for FFT

With  command  g_mindist-pi
 , select option - 1 (Protein )
In the index file protein contain information on protein ...
I got the following result..

The shortest periodic distance is 0.141718 (nm) at time 7692 (ps),
between atoms 26 and 111

Is the simulation is behaving abnormal(I.e  simulation is wrong ) or  I
 have to select the option system on prompting ??? I am very new to these
simulation field..
so all suggestion are appreciable ...



On Thu, Mar 29, 2012 at 5:05 PM, Justin A. Lemkul  wrote:

>
>
> rama david wrote:
>
>> Hi Gromacs users ,
>> as per the link given on gromacs website...
>> Introduction to Molecular Dynamics Simulations and Analysis <
>> http://nmr.chem.uu.nl/%**7Etsjerk/course/molmod/>
>> - Tutorial for performing and analyzing simulations of proteins. Includes
>> examples of many of the gromacs analysis tools and addresses a number of
>> issues that are commonly raised on the GROMACS user list. This tutorial
>> uses GROMACS version 3.3.1 (Tsjerk A. Wassenaar).
>>
>>
>>
>> editconf -f protein-EM-vacuum.pdb -o protein-PBC.gro -bt dodecahedron -d
>> 1.0
>>
>> mdp file parameter are as follow ,
>>
>> coulombtype  = Reaction-Field
>> rcoulomb = 1.4
>> epsilon_rf   = 78
>> epsilon_r= 1
>> vdw-type = Cut-off
>> rvdw = 1.4
>>  so my query  is ..
>>
>> As mention in manual ...
>> (Page no 14  manual 4.5.4  I am using the Gromacs 4.5.4  )
>> *This means that the length of each box vector must exceed the length of
>> the macromolecule in the
>> direction of that edge plus two times the cut-off radius Rc *.
>>
>
> Read the next sentence in the manual.
>
> /In  the tutorial  -d 1.0  is less than 1.4  ./..
>>
>>  I noticed that manual version and tutorial  gromacs version are
>> different ...
>> But it raise a lot of confusion  for new users like me..
>>  1. Is the -d .. should be equal  or more than cutt off ???
>> or
>>  Is the -d   .. should be equal or more than cutt-off??
>>
>>
> The basic point is that in all simulations you have to avoid the same
> molecule "seeing" itself across a periodic boundary.  So in reality, you
> need a periodic distance (which is equivalent to the value set with -d,
> times 2) that exceeds the longest cutoff.  Assuming the unit cell does not
> undergo massive shrinking, this value is generally pretty stable in an
> aqueous environment.  Setting -d 1.0 is common because it creates a 2.0-nm
> distance between a centered solute, which exceeds your cutoff and is
> sufficient to avoid the influence of water ordering, as discussed recently:
> http://lists.gromacs.org/**pipermail/gmx-users/2012-**March/069617.html
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> h

Re: [gmx-users] Not able to continue with Equilibration

[francesca vitalini]

Hi!
I'm having a similar problem. I have a dimer solvated in a big box of
water plus ions that I have managed to minimize correctly (see output
of minimization at the end) but when I try to run NVT equilibration
(see later) I get LINCS warnings(see below) refearred to atoms which
are not in a cluster or in a strange position. I have added dihedral
restraints on them but still the same type of error. I'm using GROMACS
3.3.1. I have tried to switch to a newer version of GROMACS but still
the same error.
Does anyone have any suggestions?
Thanks
Francesca


MINIMIZATION OUTPUT

Steepest Descents converged to Fmax < 1000 in 681 steps
Potential Energy  = -1.9597512e+07
Maximum force =  2.4159846e+02 on atom 13087
Norm of force =  2.1520395e+04


MINIMIZATION.MDP

define = -DEFLEXIBLE ; flexible water
integrator  = steep ; Algorithm (steep = steepest descent
minimization)
emtol   = 1000.0 ; Stop minimization when the maximum
force < 1000.0 kJ/mol/nm
emstep  = 0.001  ; Energy step size
nsteps  = 5 ; Maximum number of (minimization)
steps to perform

; 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
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   ; Short-range electrostatic cut-off
rvdw= 1.0   ; Short-range Van der Waals cut-off
pbc = xyz   ; Periodic Boundary Conditions (yes/no)


NVT.MDP

define  = -DPOSRES  ; position restrain the protein
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 1 ; 2 * 1 = 20 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 50; save coordinates every 0.2 ps
nstvout = 50; save velocities every 0.2 ps
nstenergy   = 50; save energies every 0.2 ps
nstlog  = 50; update log file every 0.2 ps
; Bond parameters
unconstrained_start = no
;continuation   = no; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist   = 3.0   ; short-range neighborlist cutoff (in nm)
rcoulomb= 3.0   ; short-range electrostatic cutoff (in nm)
rvdw= 3.0   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = berendsen ; modified Berendsen thermostat
tc-grps = Protein Non-Protein   ; two coupling groups - more accurate
tau_t   = 0.1 0.1   ; time constant, in ps
ref_t   = 300 300   ; reference temperature, one
for each group, in K
; Pressure coupling is off
pcoupl  = no; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; assign velocities from Maxwell distribution
gen_temp= 300   ; temperature for Maxwell distribution
gen_seed= -1; generate a random seed

; Dihedral restraints

dihre   =  simple ; Some dihedrals are restrained  for
instance peptide bonds are set to trans conformation.
dihre_fc=  500
dihre_tau   =  0.0
nstdihreout =  50

NVT LINCS ERROR

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.002851 (between atoms 10721 and 10723) rms 0.000161
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
672673   33.70.1000   0.1000  0.1000
   1081   1082   33.80.1000   0.1000  0.1000
   1647   1648   34.40.1000   0.1000  0.1000
   2819   2820   37.10.1000   0.1000  0.1000
   2920   2921   39.60.1000   0.1000  0.1000
   4090   4091   35.20.1000   0.1000  0.1000
   4727   4728   37.20.1000   0.1000  0.1000
   5160   5161   31.70.1000   0.1000  0.1000
   6824   6825   33.30.1000   0.1000  0.1000
...
step 0
Step 1, time 0.002 (ps)  LINCS

Re: [gmx-users] Not able to continue with Equilibration

[Mark Abraham]

On 29/03/2012 8:22 PM, Hendry wrote:


Hi,

I am using Gromacs 4.5.4. After successful minimization by SD, I 
continued with equilibration step but I got the below errors. I tried 
many times with different parameters but the problem still persists. I 
have given errors and md parameters of equilibration step below. I 
have also provided my minimization output at the end. Could you 
provide some suggestions what went wrong?.




You are using PR-pressure coupling for equilibration, which is an 
unstable combination. You are coupling ions to their own thermostat, 
which is unstable. Do check out the GROMACS manual for discussion of how 
these algorithms work, and also the website for some practical observations.


Mark
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Re: [gmx-users] mpirun

[Mark Abraham]

On 29/03/2012 8:09 PM, cuong nguyen wrote:

Dear Gromacs Users,

as in the manual, I tried to run the simulation on 4 processors and 
used the command as follow:
/mpirun -np 4 mdrun_mpi -s NVT_50ns -o NVT_50ns -c NVT_50ns.g96 -x 
NVT_50ns -e NVT_50ns -g NVT_50ns -v/


Then I got the error:
/mpirun was unable to launch the specified application as it could not 
find an executable:


Executable: mdrun_mpi/
Please help me to deal with this problem.


http://www.gromacs.org/Documentation/Installation_Instructions#Getting_access_to_GROMACS_after_installation 



Mark
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Re: [gmx-users] About cutt-off scheme ..

[Justin A. Lemkul]

rama david wrote:

Hi Gromacs users ,
as per the link given on gromacs website...
Introduction to Molecular Dynamics Simulations and Analysis 
 - Tutorial for 
performing and analyzing simulations of proteins. Includes examples of 
many of the gromacs analysis tools and addresses a number of issues that 
are commonly raised on the GROMACS user list. This tutorial uses GROMACS 
version 3.3.1 (Tsjerk A. Wassenaar).



editconf -f protein-EM-vacuum.pdb -o protein-PBC.gro -bt dodecahedron -d 
1.0


mdp file parameter are as follow ,

coulombtype  = Reaction-Field
rcoulomb = 1.4
epsilon_rf   = 78
epsilon_r= 1
vdw-type = Cut-off
rvdw = 1.4
 
 so my query  is ..


As mention in manual ...
(Page no 14  manual 4.5.4  I am using the Gromacs 4.5.4  )
*This means that the length of each box vector must exceed the length of 
the macromolecule in the

direction of that edge plus two times the cut-off radius Rc *.


Read the next sentence in the manual.


/In  the tutorial  -d 1.0  is less than 1.4  ./..
 I noticed that manual version and tutorial  gromacs version are 
different ...

But it raise a lot of confusion  for new users like me..
 
1. Is the -d .. should be equal  or more than cutt off ???

 or
 Is the -d   .. should be equal or more than cutt-off??



The basic point is that in all simulations you have to avoid the same molecule 
"seeing" itself across a periodic boundary.  So in reality, you need a periodic 
distance (which is equivalent to the value set with -d, times 2) that exceeds 
the longest cutoff.  Assuming the unit cell does not undergo massive shrinking, 
this value is generally pretty stable in an aqueous environment.  Setting -d 1.0 
is common because it creates a 2.0-nm distance between a centered solute, which 
exceeds your cutoff and is sufficient to avoid the influence of water ordering, 
as discussed recently: 
http://lists.gromacs.org/pipermail/gmx-users/2012-March/069617.html


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] deformations aplying an electric field

[Rebeca García Fandiño]

Hi,
I am trying to simulate a nanotube inserted into a lipid bilayer using Gromacs 
4, applying an external electric field (in the direction of the z axis).
I have added this line to my input file:
;Electric field
E_z = 1  1.0  0 

The calculations finish without problem, however I can see a big deformation 
both of the nanotube and also of the membrane. Is this normal? When I use a 
smaller electric field:
E_z = 1  0.01  0

I cannot see these deformations.

Is it usual to find deformations using high electric fields such as 1V?

Thanks a lot in advance.

Best wishes,

Dr. Rebeca Garcia
Santiago de Compostela University
Spain
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[gmx-users] About cutt-off scheme ..

[rama david]

Hi Gromacs users ,
as per the link given on gromacs website...
Introduction to Molecular Dynamics Simulations and
Analysis- Tutorial for
performing and analyzing simulations of proteins. Includes
examples of many of the gromacs analysis tools and addresses a number of
issues that are commonly raised on the GROMACS user list. This tutorial
uses GROMACS version 3.3.1 (Tsjerk A. Wassenaar).


editconf -f protein-EM-vacuum.pdb -o protein-PBC.gro -bt dodecahedron -d
1.0

mdp file parameter are as follow ,

coulombtype  = Reaction-Field
rcoulomb = 1.4
epsilon_rf   = 78
epsilon_r= 1
vdw-type = Cut-off
rvdw = 1.4

 so my query  is ..

As mention in manual ...
(Page no 14  manual 4.5.4  I am using the Gromacs 4.5.4  )
*This means that the length of each box vector must exceed the length of
the macromolecule in the
direction of that edge plus two times the cut-off radius Rc *.
*In  the tutorial  -d 1.0  is less than 1.4  .*..
 I noticed that manual version and tutorial  gromacs version are different
...
But it raise a lot of confusion  for new users like me..

1. Is the -d .. should be equal  or more than cutt off ???
 or
 Is the -d   .. should be equal or more than cutt-off??
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Re: [gmx-users] Not able to continue with Equilibration

[Hendry]

Dear Felix,

Thanks for suggestions. I will try it now.



On Thu, Mar 29, 2012 at 5:40 PM, Rausch, Felix  wrote:

>  Hello,
>
> ** **
>
> The results of the energy minimization look reasonable. Nevertheless, you
> should (visually) check your equilibration starting structure for problems
> (e.g. clashes that could not be solved by EM). It would be a good idea to
> concentrate on the atom numbers given in the error messages.
>
> ** **
>
> To prevent the “exploding” system during equilibration, reducing the time
> step may be a good idea. Or you could start with a short NVT run first to
> equilibrate the temperature before switching to NPT. Furthermore, the
> coupling of ions in a single thermostat group is in general not a good idea
> (search the mailing list for many discussions about this topic).
>
> ** **
>
> Good luck.
>
> ** **
>
> *Von:* gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
> *Im Auftrag von *Hendry
> *Gesendet:* Donnerstag, 29. März 2012 11:25
> *An:* Discussion list for GROMACS users
> *Betreff:* [gmx-users] Not able to continue with Equilibration
>
> ** **
>
> Hi,
>
>  
>
> I am using Gromacs 4.5.4. After successful minimization by SD, I continued
> with equilibration step but I got the below errors. I tried many times with
> different parameters but the problem still persists. I have given errors
> and md parameters of equilibration step below. I have also provided my
> minimization output at the end. Could you provide some suggestions what
> went wrong?. 
>
>  
>
> Many thanks
>
>  
>
> Sincerely
>
> Hendry   
>
>  
>
> *Errors:*
>
> Warning: 1-4 interaction between 2969 and 2974 at distance 5.543 which is
> larger than the 1-4 table size 2.400 nm
>
> These are ignored for the rest of the simulation
>
> This usually means your system is exploding,
>
> if not, you should increase table-extension in your mdp file
>
> or with user tables increase the table size
>
>  
>
> Step 1, time 0.002 (ps)  LINCS WARNING
>
> relative constraint deviation after LINCS:
>
> rms 92.242942, max 9194.071289 (between atoms 3025 and 3024)
>
> bonds that rotated more than 30 degrees:
>
>  atom 1 atom 2  angle  previous, current, constraint length
>
>2987   2973  106.31.3892   7.3433  0.1530
>
>2974   2973  174.81.1940   7.7482  0.1530
>
>2975   2974   79.90.1865   1.4460  0.1530
>
>2978   2975   98.50.1423   0.6164  0.1390
>
>2982   2978   86.10.1421   0.6512  0.1390
>
>2979   2978   89.80.1114   5.2456  0.1090
>
>2989   2987  132.20.1781   2.6697  0.1330
>
>2988   2987  142.20.2284   2.7180  0.1230
>
>2971   2969   62.97.0921   3.5084  0.1330
>
>2970   2969   88.16.8598   4.7791  0.1230
>
>2973   2971  120.62.8109   8.8274  0.1470
>
>2972   2971  165.62.0293   6.9953  0.1000
>
>3016   3013  103.10.5628  65.6450  0.1390
>
>3014   3013   39.00.3331   5.0018  0.1330
>
>3017   3014   81.60.1827  57.9252  0.1330
>
>3015   3014   77.90.0752   6.3613  0.1090
>
>3020   3016   81.32.2255  79.7378  0.1390
>
>3019   3016  100.90.4862  54.4883  0.1390
>
>3019   3017   79.30.1679  57.8415  0.1330
>
>3018   3017   94.50.1686  66.3440  0.1000
>
>3022   3019   87.70.5657   7.7539  0.1390
>
>3026   3022  104.50.8085  54.9923  0.1390
>
>3023   3022   87.40.6108   5.0641  0.1090
>
>2968   2964  174.11.5617   5.1413  0.1470
>
>2965   2964   59.55.2178   4.0658  0.1470
>
>2969   2965   35.57.6693   2.9000  0.1530
>
>2966   2965  137.35.3225   4.6157  0.1530
>
>2967   2966  150.31.6016   1.7332  0.1530
>
>2968   2967   72.40.1685   1.8310  0.1530
>
>3026   3024   94.80.8572  96.6156  0.1390
>
>3025   3024   89.90.6811 1002.2628  0.1090
>
>3027   3026  108.01.1638  47.5384  0.1090
>
>2991   2989  138.20.2045   0.6556  0.1470
>
>2990   2989  157.00.1236   0.7213  0.1000
>
>2998   2991   89.90.1961   0.9471  0.1530
>
>2992   2991   79.50.1931   0.5434  0.1530
>
>2993   2992   49.80.1577   0.1862  0.1530
>
>3000   2998   84.90.1463   0.5492  0.1330
>
>2999   2998   83.30.1346   0.5372  0.1230
>
>3002   3000   44.20.1535   0.2150  0.1470
>
>3003   3002   31.60.1548   0.1834  0.1530
>
>3009   3007   62.40.1507   0.3181  0.1330
>
>3008   3007   44.10.1280   0.1578  0.1230
>
>3011   3009   80.30.2401   1.9894  0.1470
>
>   

AW: [gmx-users] Not able to continue with Equilibration

[Rausch, Felix]

Hello,

The results of the energy minimization look reasonable. Nevertheless, you 
should (visually) check your equilibration starting structure for problems 
(e.g. clashes that could not be solved by EM). It would be a good idea to 
concentrate on the atom numbers given in the error messages.

To prevent the "exploding" system during equilibration, reducing the time step 
may be a good idea. Or you could start with a short NVT run first to 
equilibrate the temperature before switching to NPT. Furthermore, the coupling 
of ions in a single thermostat group is in general not a good idea (search the 
mailing list for many discussions about this topic).

Good luck.

Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im 
Auftrag von Hendry
Gesendet: Donnerstag, 29. März 2012 11:25
An: Discussion list for GROMACS users
Betreff: [gmx-users] Not able to continue with Equilibration

Hi,

I am using Gromacs 4.5.4. After successful minimization by SD, I continued with 
equilibration step but I got the below errors. I tried many times with 
different parameters but the problem still persists. I have given errors and md 
parameters of equilibration step below. I have also provided my minimization 
output at the end. Could you provide some suggestions what went wrong?.

Many thanks

Sincerely
Hendry

Errors:
Warning: 1-4 interaction between 2969 and 2974 at distance 5.543 which is 
larger than the 1-4 table size 2.400 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

Step 1, time 0.002 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 92.242942, max 9194.071289 (between atoms 3025 and 3024)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2987   2973  106.31.3892   7.3433  0.1530
   2974   2973  174.81.1940   7.7482  0.1530
   2975   2974   79.90.1865   1.4460  0.1530
   2978   2975   98.50.1423   0.6164  0.1390
   2982   2978   86.10.1421   0.6512  0.1390
   2979   2978   89.80.1114   5.2456  0.1090
   2989   2987  132.20.1781   2.6697  0.1330
   2988   2987  142.20.2284   2.7180  0.1230
   2971   2969   62.97.0921   3.5084  0.1330
   2970   2969   88.16.8598   4.7791  0.1230
   2973   2971  120.62.8109   8.8274  0.1470
   2972   2971  165.62.0293   6.9953  0.1000
   3016   3013  103.10.5628  65.6450  0.1390
   3014   3013   39.00.3331   5.0018  0.1330
   3017   3014   81.60.1827  57.9252  0.1330
   3015   3014   77.90.0752   6.3613  0.1090
   3020   3016   81.32.2255  79.7378  0.1390
   3019   3016  100.90.4862  54.4883  0.1390
   3019   3017   79.30.1679  57.8415  0.1330
   3018   3017   94.50.1686  66.3440  0.1000
   3022   3019   87.70.5657   7.7539  0.1390
   3026   3022  104.50.8085  54.9923  0.1390
   3023   3022   87.40.6108   5.0641  0.1090
   2968   2964  174.11.5617   5.1413  0.1470
   2965   2964   59.55.2178   4.0658  0.1470
   2969   2965   35.57.6693   2.9000  0.1530
   2966   2965  137.35.3225   4.6157  0.1530
   2967   2966  150.31.6016   1.7332  0.1530
   2968   2967   72.40.1685   1.8310  0.1530
   3026   3024   94.80.8572  96.6156  0.1390
   3025   3024   89.90.6811 1002.2628  0.1090
   3027   3026  108.01.1638  47.5384  0.1090
   2991   2989  138.20.2045   0.6556  0.1470
   2990   2989  157.00.1236   0.7213  0.1000
   2998   2991   89.90.1961   0.9471  0.1530
   2992   2991   79.50.1931   0.5434  0.1530
   2993   2992   49.80.1577   0.1862  0.1530
   3000   2998   84.90.1463   0.5492  0.1330
   2999   2998   83.30.1346   0.5372  0.1230
   3002   3000   44.20.1535   0.2150  0.1470
   3003   3002   31.60.1548   0.1834  0.1530
   3009   3007   62.40.1507   0.3181  0.1330
   3008   3007   44.10.1280   0.1578  0.1230
   3011   3009   80.30.2401   1.9894  0.1470
   3010   3009   82.90.1141   0.3157  0.1000
   3028   3011   85.20.2391   1.9233  0.1530
   3012   3011   97.90.3034   4.9831  0.1530
   3013   3012   82.40.3759   7.3991  0.1530
   3024   3020   85.62.4674  98.3412  0.1390
   3021   3020   81.01.2452  66.1375  0.1090
   3030   3028   88.90.1492   0.2673  0.1330
   3029   3028   61.20.1379   0.2407  0.1230
  49372  49371   89.50.1000 221.0566  0.1000
  49373  49371   92.40.1000 170.7231  0.1000
   2956   2954  153.40.1550   3.5621  0.1470
   2955   2954  135.50.1246   0.8967  0.1000
   2962   2956   76.60.7151   5.0532  0.1530
   2957   2956  178.70.1220   3.9773  0.1530
   2958   2957  155.0

Re: [gmx-users] mpirun

[TH Chew]

Where did you install your Gromacs? Most likely the executables are not in
the PATH.

On Thu, Mar 29, 2012 at 5:09 PM, cuong nguyen  wrote:

> Dear Gromacs Users,
>
> as in the manual, I tried to run the simulation on 4 processors and used
> the command as follow:
> *mpirun -np 4 mdrun_mpi -s NVT_50ns -o NVT_50ns -c NVT_50ns.g96 -x
> NVT_50ns -e NVT_50ns -g NVT_50ns -v*
>
> Then I got the error:
> *mpirun was unable to launch the specified application as it could not
> find an executable:
>
> Executable: mdrun_mpi*
> Please help me to deal with this problem.
>
> Best regards,
>
>
> Nguyen Van Cuong
> PhD student - Curtin University of Technology
> Mobile: (+61) 452213981
>
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> 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/Support/Mailing_Lists
>



-- 
Regards,
THChew
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[gmx-users] Not able to continue with Equilibration

[Hendry]

Hi,



I am using Gromacs 4.5.4. After successful minimization by SD, I continued
with equilibration step but I got the below errors. I tried many times with
different parameters but the problem still persists. I have given errors
and md parameters of equilibration step below. I have also provided my
minimization output at the end. Could you provide some suggestions what
went wrong?.



Many thanks



Sincerely

Hendry



*Errors:*

Warning: 1-4 interaction between 2969 and 2974 at distance 5.543 which is
larger than the 1-4 table size 2.400 nm

These are ignored for the rest of the simulation

This usually means your system is exploding,

if not, you should increase table-extension in your mdp file

or with user tables increase the table size



Step 1, time 0.002 (ps)  LINCS WARNING

relative constraint deviation after LINCS:

rms 92.242942, max 9194.071289 (between atoms 3025 and 3024)

bonds that rotated more than 30 degrees:

 atom 1 atom 2  angle  previous, current, constraint length

   2987   2973  106.31.3892   7.3433  0.1530

   2974   2973  174.81.1940   7.7482  0.1530

   2975   2974   79.90.1865   1.4460  0.1530

   2978   2975   98.50.1423   0.6164  0.1390

   2982   2978   86.10.1421   0.6512  0.1390

   2979   2978   89.80.1114   5.2456  0.1090

   2989   2987  132.20.1781   2.6697  0.1330

   2988   2987  142.20.2284   2.7180  0.1230

   2971   2969   62.97.0921   3.5084  0.1330

   2970   2969   88.16.8598   4.7791  0.1230

   2973   2971  120.62.8109   8.8274  0.1470

   2972   2971  165.62.0293   6.9953  0.1000

   3016   3013  103.10.5628  65.6450  0.1390

   3014   3013   39.00.3331   5.0018  0.1330

   3017   3014   81.60.1827  57.9252  0.1330

   3015   3014   77.90.0752   6.3613  0.1090

   3020   3016   81.32.2255  79.7378  0.1390

   3019   3016  100.90.4862  54.4883  0.1390

   3019   3017   79.30.1679  57.8415  0.1330

   3018   3017   94.50.1686  66.3440  0.1000

   3022   3019   87.70.5657   7.7539  0.1390

   3026   3022  104.50.8085  54.9923  0.1390

   3023   3022   87.40.6108   5.0641  0.1090

   2968   2964  174.11.5617   5.1413  0.1470

   2965   2964   59.55.2178   4.0658  0.1470

   2969   2965   35.57.6693   2.9000  0.1530

   2966   2965  137.35.3225   4.6157  0.1530

   2967   2966  150.31.6016   1.7332  0.1530

   2968   2967   72.40.1685   1.8310  0.1530

   3026   3024   94.80.8572  96.6156  0.1390

   3025   3024   89.90.6811 1002.2628  0.1090

   3027   3026  108.01.1638  47.5384  0.1090

   2991   2989  138.20.2045   0.6556  0.1470

   2990   2989  157.00.1236   0.7213  0.1000

   2998   2991   89.90.1961   0.9471  0.1530

   2992   2991   79.50.1931   0.5434  0.1530

   2993   2992   49.80.1577   0.1862  0.1530

   3000   2998   84.90.1463   0.5492  0.1330

   2999   2998   83.30.1346   0.5372  0.1230

   3002   3000   44.20.1535   0.2150  0.1470

   3003   3002   31.60.1548   0.1834  0.1530

   3009   3007   62.40.1507   0.3181  0.1330

   3008   3007   44.10.1280   0.1578  0.1230

   3011   3009   80.30.2401   1.9894  0.1470

   3010   3009   82.90.1141   0.3157  0.1000

   3028   3011   85.20.2391   1.9233  0.1530

   3012   3011   97.90.3034   4.9831  0.1530

   3013   3012   82.40.3759   7.3991  0.1530

   3024   3020   85.62.4674  98.3412  0.1390

   3021   3020   81.01.2452  66.1375  0.1090

   3030   3028   88.90.1492   0.2673  0.1330

   3029   3028   61.20.1379   0.2407  0.1230

  49372  49371   89.50.1000 221.0566  0.1000

  49373  49371   92.40.1000 170.7231  0.1000

   2956   2954  153.40.1550   3.5621  0.1470

   2955   2954  135.50.1246   0.8967  0.1000

   2962   2956   76.60.7151   5.0532  0.1530

   2957   2956  178.70.1220   3.9773  0.1530

   2958   2957  155.00.2036   1.2639  0.1530

   2961   2959   34.50.1265   0.1186  0.1250

   2960   2959   30.40.1264   0.1346  0.1250

   2964   2962  114.91.7422   7.9205  0.1330

   2963   2962  156.90.4832   6.1127  0.1230

  53158  53157   90.00.1000   0.1575  0.1000

  53159  53157   90.00.1000   0.1747  0.1000

  53386  53385   90.00.1000   0.1537  0.1000

  53387  53385   56.50.1000   0.0962  0.1000

   2954   2952   68.70.1615   0.7870  0.1330



Back Off! I just backed up step1b_n2.pdb to ./#step1b_n2.pdb.1#



Back Off! I just backed up step1c_n2.pdb to ./#step1c_n2.pdb.1#

Wrote pdb files with previous and current coordinates



---

Program mdrun, VERSION 4.5.4

Source code file: pme.c, line: 538



Fata

[gmx-users] mpirun

[cuong nguyen]

Dear Gromacs Users,

as in the manual, I tried to run the simulation on 4 processors and used
the command as follow:
*mpirun -np 4 mdrun_mpi -s NVT_50ns -o NVT_50ns -c NVT_50ns.g96 -x NVT_50ns
-e NVT_50ns -g NVT_50ns -v*

Then I got the error:
*mpirun was unable to launch the specified application as it could not find
an executable:

Executable: mdrun_mpi*
Please help me to deal with this problem.

Best regards,


Nguyen Van Cuong
PhD student - Curtin University of Technology
Mobile: (+61) 452213981
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Re: [gmx-users] Calculate Bulk Pressure Tensor?

[Erik Marklund]

29 mar 2012 kl. 04.10 skrev Weilong Zhao:

> Hi,
> 
> I was trying to calculate the pressure tensors for one of my solid crystal 
> systems. I notice that g_energy does have this option---pressure xx, pressure 
> yy and pressure zz, however the results seem to be a function of running 
> time. How can I extract information about pressure tensor at different 
> position of my solid system? If gromacs allows me to do so, do I need to 
> integrate the tensor value from one position to another position?
> Thanks very much for reading! Your kind help is greatly appreciated.
> 

I don't think that's possible, considering how gromacs calculates the pressure 
from the virial. See section 4.8.2 of the manual.

Erik

> -- 
> Weilong Zhao
> Graduate Student
> Department of Polymer Science
> University of Akron
> Akron, OH 44325
> 
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---
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html

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Re: [gmx-users] Shima Arasteh wants to share a link | Gromacs

[Shima Arasteh]

Thanks Rama,
I will do the instructions and do my best.
 
Cheers,
Shima
 


 From: rama david 
To: Discussion list for GROMACS users  
Sent: Thursday, March 29, 2012 12:57 PM
Subject: Re: [gmx-users] Shima Arasteh wants to share a link | Gromacs
  

Hi shima 
    Read the insttruction carefully ..
DELETE ALL THE LINE AND SUBSEQUENT LINES IN THE SECTION 
Delete all the bellow line in that section...
It will surely solve your problem (As I also Face the same one )
with best wishes,



On Thu, Mar 29, 2012 at 11:23 AM, ros...@kth.se  wrote:

Shima Arasteh wants to a share a link on the Gromacs wiki: 
http://www.gromacs.org/
>
>Shima Arasteh says:
>Dear Gromacs friends,
>I am a new user of Gromacs, following the kalp-15 in DPPC tutorial instruction 
>but I face a fatal error when I enter this command:
>grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr
>
>And the fatal error is this:
>atomtype LC3 not found
>
>Anybody can suggest me a solution to solve my problem?
>
>Thanks in advance
>Shima
>---
>This email was sent at the request of a user - please do not respond to this 
>email.
>
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>

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Re: [gmx-users] about g_mindist....

[Mark Abraham]

On 29/03/2012 7:20 PM, rama david wrote:

Hi everybody ,
 I run simulation of 4 same  molecule keep apart in box
of 4 4 4 dimension ..( 71 atom in one molecule = 71 * 4 = total atom 
are 284 )

force field = gromacs96   53a6

COM (center of mass) infirmation of molecules
system size :  1.255  1.577  1.883
box vectors :  4.000   4.000   4.000 (nm)
 mol1  : 2.0570.844  1.941
 mol 2  :  2.057  0.844  3.141
 mol 3  : 2.057   3.244   0.744
 mol 4  : 2.057   3.244   3.141

(Four molecule are kept at the four corner of square
 of each side 2.4 nm
four molecule are catenated in same pdb)


No they're not starting on a square. Look at those z coordinates above.



 my md.mdp input is like the ..

;Neighborsearching
ns_type= grid; search neighboring grid cells
nstlist= 5; 10 fs
rlist= 1.0; short-range neighborlist cutoff (in nm)
rcoulomb= 1.0; short-range electrostatic cutoff (in nm)
rvdw= 1.0; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype= PME; Particle Mesh Ewald for long-range 
electrostatics

pme_order= 4; cubic interpolation
fourierspacing= 0.16; grid spacing for FFT

With  command  g_mindist , select option - 1 (Protein )
I got the following result..

The shortest periodic distance is 0.141718 (nm) at time 7692 (ps),
between atoms 26 and 111

Is the simulation is behaving abnormal(I.e  simulation is wrong ) or  I
 have to select the option system on prompting ??? I am very new to 
these simulation field..

so all suggestion are appreciable ...


Shrug. You've measured the inter-group distance between a group and 
itself. Curiously enough, that's the length of a C-C bond, or similar. 
g_mindist -h is required reading. Also, we don't even know what's in 
group Protein, or your g_mindist command line.


Mark
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Re: [gmx-users] Shima Arasteh wants to share a link | Gromacs

[rama david]

Hi shima
Read the insttruction carefully ..
DELETE ALL THE LINE AND SUBSEQUENT LINES IN THE SECTION 
Delete all the bellow line in that section...
It will surely solve your problem (As I also Face the same one )
with best wishes,


On Thu, Mar 29, 2012 at 11:23 AM, ros...@kth.se  wrote:

> Shima Arasteh wants to a share a link on the Gromacs wiki:
> http://www.gromacs.org/
>
> Shima Arasteh says:
> Dear Gromacs friends,
> I am a new user of Gromacs, following the kalp-15 in DPPC tutorial
> instruction but I face a fatal error when I enter this command:
> grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr
>
> And the fatal error is this:
> atomtype LC3 not found
>
> Anybody can suggest me a solution to solve my problem?
>
> Thanks in advance
> Shima
> ---
> This email was sent at the request of a user - please do not respond to
> this email.
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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[gmx-users] about g_mindist....

[rama david]

Hi everybody ,
 I run simulation of 4 same  molecule keep apart in box
of 4 4 4 dimension ..( 71 atom in one molecule = 71 * 4 = total atom are
284 )
force field = gromacs96   53a6

COM (center of mass) infirmation of molecules
system size :  1.255  1.577  1.883
box vectors :  4.000   4.000   4.000 (nm)
 mol1  : 2.0570.844  1.941
 mol 2  :  2.057  0.844  3.141
 mol 3  : 2.057   3.244   0.744
 mol 4  : 2.057   3.244   3.141

(Four molecule are kept at the four corner of square
 of each side 2.4 nm
four molecule are catenated in same pdb)

 my md.mdp input is like the ..

;Neighborsearching
ns_type= grid; search neighboring grid cells
nstlist= 5; 10 fs
rlist= 1.0; short-range neighborlist cutoff (in nm)
rcoulomb= 1.0; short-range electrostatic cutoff (in nm)
rvdw= 1.0; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype= PME; Particle Mesh Ewald for long-range
electrostatics
pme_order= 4; cubic interpolation
fourierspacing= 0.16; grid spacing for FFT

With  command  g_mindist , select option - 1 (Protein )
I got the following result..

The shortest periodic distance is 0.141718 (nm) at time 7692 (ps),
between atoms 26 and 111

Is the simulation is behaving abnormal(I.e  simulation is wrong ) or  I
 have to select the option system on prompting ??? I am very new to these
simulation field..
so all suggestion are appreciable ...
-- 
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RE: [gmx-users] Shima Arasteh wants to share a link | Gromacs

[Emanuel Birru]

Check your topology file. The atom LC3 is not found in Gromacs .atp file. 

How did you generate your .top file? If you generate it using pdb2gmx it should 
not give you such error.


Cheers,







=
Emmanuel Birru
PhD Candidate

Faculty of Pharmacy and Pharmaceutical Sciences
Monash University (Parkville Campus)
381 Royal Parade, Parkville
Victoria 3052, Australia

Tel: Int + 61 3 9903 9187
E-mail: emanuel.bi...@monash.edu 
www.pharm.monash.edu.au


-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of ros...@kth.se
Sent: Thursday, 29 March 2012 4:53 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] Shima Arasteh wants to share a link | Gromacs

Shima Arasteh wants to a share a link on the Gromacs wiki: 
http://www.gromacs.org/

Shima Arasteh says:
Dear Gromacs friends,
I am a new user of Gromacs, following the kalp-15 in DPPC tutorial instruction 
but I face a fatal error when I enter this command:
grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr

And the fatal error is this:
atomtype LC3 not found

Anybody can suggest me a solution to solve my problem?

Thanks in advance
Shima
---
This email was sent at the request of a user - please do not respond to this 
email.

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Re: [gmx-users] Shima Arasteh wants to share a link | Gromacs

[Mark Abraham]

On 29/03/2012 4:53 PM, ros...@kth.se wrote:

Shima Arasteh wants to a share a link on the Gromacs wiki: 
http://www.gromacs.org/

Shima Arasteh says:
Dear Gromacs friends,
I am a new user of Gromacs, following the kalp-15 in DPPC tutorial instruction 
but I face a fatal error when I enter this command:
grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr

And the fatal error is this:
atomtype LC3 not found

Anybody can suggest me a solution to solve my problem?


You've done something wrong, unless you're the first person to correctly 
follow a wrong tutorial :-) A [moleculetype] is referencing an 
[atomtype] that your force field has not defined. Go back and try again.


Mark
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Re: [gmx-users] Pressure coupling doubt

[Mark Abraham]

On 29/03/2012 5:38 PM, bipin singh wrote:

Hello,

I have two doubts regarding pressure coupling in Gromacs:

1) When I use pcoupl=no

the mdp.out shows the following

; Pressure coupling
pcoupl   = no
Pcoupltype   = Isotropic
nstpcouple   = -1
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau-p= 1
compressibility  =
ref-p=

I have not used the pcoupl(=no) then why it is showing Pcoupltype=Isotropic.


... because that was either the value you input, or the default value. 
Neither matters, because you said not to use pressure coupling.





(2) This is a silly question: What will happen if we use following
option in mdp of NVT simulation:

  pcoupl=no
  compressibility= 4.5e-5

does it will affect the NVT criteria ? or It will ignore the
compressibility input?


It will ignore it.

Mark
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Re: [gmx-users] About movie in GROMACS

[Mark Abraham]

On 29/03/2012 4:15 PM, rama david wrote:

HI Gromacs Friends,
 I complete one simulation for 4 different molecule  
placed apart

in box of  dimension 4 4 4 ..
when I used the trajectory I saw the one molecule interact with each 
other but they are

getting broken because of box..(Some part protruding from other side).
To see movie I used the command
1. trjconv -s ..tpr  -f ..xtc  -o movie.pdb -pbc nojump -dt 10
 The molecules moving apart without any interaction

2. trjconv -s ..tpr  -f ..xtc  -o movie.pdb -pbc whole -dt 10
 The molecules are interacting in cell ..
  but because of periodic cell , near the cell boundary  the molecule
 interaction get remove and molecules come in cell from other side..
( I know it is because of periodic boundary condition ..one goes 
from right

  hand side come in cell through left hand side )

To see the four molecule interacting each other near also cell 
boundary , what command

I have to use ???


It depends. See suggested workflow here: 
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions. 
There is no general solution for an arbitrary trajectory to look nice. 
There need not even be a solution for a specific trajectory to look 
nice. Imagine a cluster of molecules from which one emerges, transits 
the whole simulation cell including periodic boundary, and merges again 
with the other side of the cluster. You cannot create a representation 
of the trajectory that lacks jumps and has the cluster whole when it is 
whole.


Mark
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AW: [gmx-users] About movie in GROMACS

[lloyd riggs]

>From my limited experience,

...Also, VMD makes this easier.  I learned the hard way to center on a molecule 
when making the initial box in editconf.  Otherwise varied combinations of the 
-mol, -pbc , -nojump -center options usually work, but never consitent at least 
for me.  Still, if its 4 small molecules it might not make a difference if the 
other 3 keep moving out of the box.

The only differences I noticed in analyzing these was with distances, and 
geometric math functions, in which case you would have to analyze each moleucle 
centered in the .trj (ie 3-4 different centered versions of the same initial 
.trj) seperat. All the energy and force values were independent of this though.

Good luck

Stephan Watkins

 Original-Nachricht 
> Datum: Thu, 29 Mar 2012 06:55:06 +
> Von: "Rausch, Felix" 
> An: \'Discussion list for GROMACS users\' 
> Betreff: AW: [gmx-users] About movie in GROMACS

> Hi.
> 
> Take a look at the "-center" flag of trjconv. Together with "-pbc" (and
> maybe also "-ur") it should be possible to center your molecules of interest
> in the middle of the simulation cell.
> 
> 
> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
> Im Auftrag von rama david
> Gesendet: Donnerstag, 29. März 2012 07:18
> An: Discussion list for GROMACS users
> Betreff: [gmx-users] About movie in GROMACS
> 
> HI Gromacs Friends,
>  I complete one simulation for 4 different molecule  placed
> apart
> in box of  dimension 4 4 4 ..
> when I used the trajectory I saw the one molecule interact with each other
> but they are
> getting broken because of box..(Some part protruding from other side).
> To see movie I used the command
> 1. trjconv -s ..tpr  -f ..xtc  -o movie.pdb -pbc nojump -dt 10
>  The molecules moving apart without any interaction
> 
> 2. trjconv -s ..tpr  -f ..xtc  -o movie.pdb -pbc whole -dt 10
>  The molecules are interacting in cell ..
>   but because of periodic cell , near the cell boundary  the molecule
>  interaction get remove and molecules come in cell from other side..
> ( I know it is because of periodic boundary condition ..one goes from
> right
>   hand side come in cell through left hand side )
> 
> To see the four molecule interacting each other near also cell boundary ,
> what command
> I have to use ???

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