Re: [gmx-users] About Usage of Constraints

[Justin Lemkul]

On 10/7/12 12:24 AM, vidhya sankar wrote:

Dear justin Thank you for your previous reply
 I  am 
running NPT Equlibration  at 20 ps  with dt 0.0002 in 10 steps  Without 
usage of  Lincs Algorithm and its related parameters it runs Successfully .
But When I  Increase dt from 0.0002 to 0.002 then I have got error as follows 
in grompp

WARNING 1 [file 2KDQTR.top, line 71]:
   The bond in molecule-type Protein_chain_A between atoms 1 N and 2 H1 has
   an estimated oscillational period of 1.0e-02 ps, which is less than 5
   times the time step of 2.0e-03 ps.
   Maybe you forgot to change the constraints mdp option.



One cannot arbitrarily increase the timestep to such a value without using 
constraints.  The relationship between timestep and bond vibrational frequencies 
is discussed in every major simulation textbook.



Then I have used the Lincs Algorithm and its related parameter Then I have got 
Error during Mdrun as follows I  saw  there Are Plenty Of discussion in Mailing 
list   But  I am Not Able to come to conclusion


relative constraint deviation after LINCS:
rms 0.015272, max 0.577865 (between atoms 120 and 122)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
Wrote pdb files with previous and current coordinates

129131   39.10.1475   0.1664  0.1330
 129130   37.80.1191   0.1243  0.1230
 125126   38.50.1738   0.1508  0.1530
 124129  103.20.0962   0.9157  0.1530
 124125  124.30.1725   0.8648  0.1530
 122124  169.90.4717   2.5621  0.1470
 122123  168.00.2655   3.1890  0.1000
 120122  176.30.5957   7.3414  0.1330
 120121  172.80.5550   6.4843  0.1230
What does the Above Fact Indicates I mean the Problem is in Topology or in MD 
Parameter file ?



Either, or both.  It's impossible to say without a more thorough description of 
your system, what you have done to minimize and equilibrate it, and what you're 
trying to do.  Basically everything you would be advised is already described here:


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

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] Distribution of z-coordinates for a particular index group

[Andrew DeYoung]

Hi,

My system is in the slab geometry; I have applied periodic boundary
conditions along x and y, but none along z.

I frequently use the handy tool g_potential (using the -oc switch) to
compute the (average) charge density (i.e., charge distribution or a
"histogram of charges") along z for a particular group specified by an index
file entry.  Since the partial charges are discretely assigned to individual
atoms, this means that the -oc switch of g_potential effectively gives me a
sort of distribution of the atoms along z, although the units are charge
density, of course.

My question is, what if I have atoms with zero partial charge?  Of course,
such atoms do not contribute to the charge density.  But what if I would
still like to compute some sort of distribution of these atoms along z?

One idea is to use g_traj to print all of the z-coordinates of a particular
group over time to an .xvg file. Then, using a scripting language, I could
"bin" the z-coordinates and then average over time.  But is there already a
Gromacs utility that does this?

It seems that g_density, with the "-dens number" switch, may accomplish
this.  Is it true that the "-dens number" switch will lead to computation of
the number density of _each_ atom which is specified in the index file
entry?

Thank you for your time!

Andrew DeYoung
Carnegie Mellon University

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[gmx-users] Re: Segmentation fault, mdrun_mpi

[Ladasky]

Justin Lemkul wrote
> Random segmentation faults are really hard to debug.  Can you resume the
> run 
> using a checkpoint file?  That would suggest maybe an MPI problem or
> something 
> else external to Gromacs.  Without a reproducible system and a debugging 
> backtrace, it's going to be hard to figure out where the problem is coming
> from.

Thanks for that tip, Justin.  I tried to resume one run which failed at 1.06
million cycles, and it WORKED.  It proceeded all the way to the 2.50 million
cycles that I designated.  I now have two separate .trr files, but I suppose
they can be merged.

I don't know whether my crashes are random yet.  I will try re-running that
simulation again from time zero, to see whether it segfaults at the same
place.  If it doesn't, then I have a problem which may have nothing to do
with GROMACS.

I looked in on memory usage several times while mdrun_mpi was executing. 
Over all, about 3 GB of my computer's 8 GB of RAM were in use.  As I
expected, GROMACS used very little of this.  The mpirun process used a
constant 708K.  I had five mdrun_mpi processes, all of which used slightly
more RAM as they worked, but I didn't notice anything which suggested a
gross memory leak.  The process which used the most RAM was using 14.4 MB
right after it started, rose to 15.9 MB within the first ten minutes or so,
and reached 16.0 MB after four hours.  The process which used the least RAM
started at 10.6 MB and finished at 10.8 MB.  All together, GROMACS was using
about 64 MB.

I have a well-cooled CPU, core temperatures are under 50 degrees when the
system is running under full load.  My system doesn't lock up or crash on
me.  I think that my hardware is good.




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[gmx-users] Fwd: How to can i replace a molecule

[Ali Alizadeh]

Dear All users

How to can i replace a molecule(for example methane) with another
molecule(propane)?
Number of these molecules are given and their position is random,

Can I use genbox or genion, How to do i do it?

Sincerely
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Re: [gmx-users] error in grompp

[Justin Lemkul]

On 10/7/12 8:42 PM, Nur Syafiqah Abdul Ghani wrote:

Dear All,

Fatal error:
number of coordinates in coordinate file (prot_wtr_solv.gro, 18031)
  does not match topology (control.top, 16650)

It happen when i started to minimize it by using the command

grompp -v -f minim_first.mdp -p control.top -c prot_wtr_solv.gro -o
minim_prot.tpr -zero

When i open the control.top and the prot_wtr_solv.gro file and i
startet to calculate the missing atom is about 1381 which is for my
DRG molecule..
I already edit and put the topology like below :

; Include topology for DRG
#include "solvent.itp"

[ system ]
; Name
ALZHEIMER'S DISEASE AMYLOID in water

[ molecules ]
; Compound#mols
Protein_chain_A 1
DRG1381
SOL   350

Can you guys please explain it to me why this happened..Its still cant
be minimize it yet..



The answer to this error is always the same.

http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology

You need to keep better track of the molecules in your system and adjust the 
topology accordingly.  When dealing with complex systems, you must do your own 
bookkeeping.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] Fwd: How to can i replace a molecule

[Justin Lemkul]

On 10/7/12 3:52 PM, Ali Alizadeh wrote:

Dear All users

How to can i replace a molecule(for example methane) with another
molecule(propane)?
Number of these molecules are given and their position is random,

Can I use genbox or genion, How to do i do it?



Likely you can't, as you were already advised:

http://lists.gromacs.org/pipermail/gmx-users/2012-October/075338.html

A more robust approach for dealing with mixed systems can be found here:

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

-Justin

--


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


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Re: [gmx-users] Re: Segmentation fault, mdrun_mpi

[Justin Lemkul]

On 10/7/12 2:15 PM, Ladasky wrote:

Justin Lemkul wrote

Random segmentation faults are really hard to debug.  Can you resume the
run
using a checkpoint file?  That would suggest maybe an MPI problem or
something
else external to Gromacs.  Without a reproducible system and a debugging
backtrace, it's going to be hard to figure out where the problem is coming
from.


Thanks for that tip, Justin.  I tried to resume one run which failed at 1.06
million cycles, and it WORKED.  It proceeded all the way to the 2.50 million
cycles that I designated.  I now have two separate .trr files, but I suppose
they can be merged.

I don't know whether my crashes are random yet.  I will try re-running that
simulation again from time zero, to see whether it segfaults at the same
place.  If it doesn't, then I have a problem which may have nothing to do
with GROMACS.

I looked in on memory usage several times while mdrun_mpi was executing.
Over all, about 3 GB of my computer's 8 GB of RAM were in use.  As I
expected, GROMACS used very little of this.  The mpirun process used a
constant 708K.  I had five mdrun_mpi processes, all of which used slightly
more RAM as they worked, but I didn't notice anything which suggested a
gross memory leak.  The process which used the most RAM was using 14.4 MB
right after it started, rose to 15.9 MB within the first ten minutes or so,
and reached 16.0 MB after four hours.  The process which used the least RAM
started at 10.6 MB and finished at 10.8 MB.  All together, GROMACS was using
about 64 MB.

I have a well-cooled CPU, core temperatures are under 50 degrees when the
system is running under full load.  My system doesn't lock up or crash on
me.  I think that my hardware is good.




My first guess would be a buggy MPI implementation.  I can't comment on hardware 
specs, but usually the random failures seen in mdrun_mpi are a result of some 
generic MPI failure.  What MPI are you using?


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] Distribution of z-coordinates for a particular index group

[Justin Lemkul]

On 10/7/12 12:13 PM, Andrew DeYoung wrote:

Hi,

My system is in the slab geometry; I have applied periodic boundary
conditions along x and y, but none along z.

I frequently use the handy tool g_potential (using the -oc switch) to
compute the (average) charge density (i.e., charge distribution or a
"histogram of charges") along z for a particular group specified by an index
file entry.  Since the partial charges are discretely assigned to individual
atoms, this means that the -oc switch of g_potential effectively gives me a
sort of distribution of the atoms along z, although the units are charge
density, of course.

My question is, what if I have atoms with zero partial charge?  Of course,
such atoms do not contribute to the charge density.  But what if I would
still like to compute some sort of distribution of these atoms along z?

One idea is to use g_traj to print all of the z-coordinates of a particular
group over time to an .xvg file. Then, using a scripting language, I could
"bin" the z-coordinates and then average over time.  But is there already a
Gromacs utility that does this?

It seems that g_density, with the "-dens number" switch, may accomplish
this.  Is it true that the "-dens number" switch will lead to computation of
the number density of _each_ atom which is specified in the index file
entry?



Seems about as good of an approach as any.  You can certainly come up with a 
test case and use g_density to see if it meets expectations.


-Justin

--


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


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Re: [gmx-users] Re: Fwd: How to can i replace a molecule

[Justin Lemkul]

On 10/7/12 9:17 PM, shika wrote:

Thanks Justin.

May I ask something, if i'm using the command for genbox before
minimization which is

genbox -cp protein_box.gro -cs solvent.gro -p control.top -o prot_solv.gro

next i insert water by using same command;

genbox -cp prot_solv.gro -p control.top -cs spc216.gro -o
prot_solv_wtr.gro maxsol 350

i'm using -cs for both genbox command instead of -ci -nmol, is it
wrong to use the command like that?




I don't understand why you need two invocations of genbox, but syntactically the 
commands are correct.  The -ci -nmol options are for adding molecules randomly 
in the unit cell.  The -cs option is for stacking grids of water boxes (or 
whatever other solvent you provide) within the unit cell.


-Justin




On Mon, Oct 8, 2012 at 8:59 AM, Justin Lemkul [via GROMACS]
 wrote:



On 10/7/12 3:52 PM, Ali Alizadeh wrote:

Dear All users

How to can i replace a molecule(for example methane) with another
molecule(propane)?
Number of these molecules are given and their position is random,

Can I use genbox or genion, How to do i do it?



Likely you can't, as you were already advised:

http://lists.gromacs.org/pipermail/gmx-users/2012-October/075338.html

A more robust approach for dealing with mixed systems can be found here:

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

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] Re: difference between the tabulated and Cut-off Electicstatics potentials

[xiaowu759]

Dear gmxers,
Sorry to all that pays attention to my previous post. When I looked into the
generated mdp files, I find that except the ele. potentials there is another
difference in the running parameters, namely cut-off. Now I am sure that it
is different cut-off that causes that big difference in stablized density,
which has been confirmed by another test using the same cut-off. However, I
am quite puzzling about why one different cut-off (1.0 vs. 1.26 nm) generate
such big difference and whether the cut-off value should match the one in
the tabulated potential at which the potential is zero. Could you give me
some hints, please?
Yours sincerely,
Chaofu Wu



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[gmx-users] Re: Fwd: How to can i replace a molecule

[shika]

it is because when i put

genbox -cp protein_box.gro -ci solvent.gro -nmol 1381 -p control.top
-o prot_solv.gro

the error turn out like this :

System total charge: 0.000
Grid: 17 x 16 x 14 cells
nri = 12718, nrj = 100152
Try 9119box_margin = 0.45overlap:
Killed

thats why i need to run genbox twice

On Mon, Oct 8, 2012 at 9:21 AM, Justin Lemkul [via GROMACS]
 wrote:
>
>
> On 10/7/12 9:17 PM, shika wrote:
>
>> Thanks Justin.
>>
>> May I ask something, if i'm using the command for genbox before
>> minimization which is
>>
>> genbox -cp protein_box.gro -cs solvent.gro -p control.top -o prot_solv.gro
>>
>> next i insert water by using same command;
>>
>> genbox -cp prot_solv.gro -p control.top -cs spc216.gro -o
>> prot_solv_wtr.gro maxsol 350
>>
>> i'm using -cs for both genbox command instead of -ci -nmol, is it
>> wrong to use the command like that?
>>
>>
>
> I don't understand why you need two invocations of genbox, but syntactically
> the
> commands are correct.  The -ci -nmol options are for adding molecules
> randomly
> in the unit cell.  The -cs option is for stacking grids of water boxes (or
> whatever other solvent you provide) within the unit cell.
>
> -Justin
>
>>
>>
>> On Mon, Oct 8, 2012 at 8:59 AM, Justin Lemkul [via GROMACS]
>> <[hidden email]> wrote:
>>>
>>>
>>> On 10/7/12 3:52 PM, Ali Alizadeh wrote:
 Dear All users

 How to can i replace a molecule(for example methane) with another
 molecule(propane)?
 Number of these molecules are given and their position is random,

 Can I use genbox or genion, How to do i do it?

>>>
>>> Likely you can't, as you were already advised:
>>>
>>> http://lists.gromacs.org/pipermail/gmx-users/2012-October/075338.html
>>>
>>> A more robust approach for dealing with mixed systems can be found here:
>>>
>>> http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents
>>>
>>> -Justin
>>>
>>> --
>>> 
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Research Scientist
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>> 
>>> --
>>> gmx-users mailing list[hidden email]
>>> 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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>>> www interface or send it to [hidden email].
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>>>
>>>
>>> 
>>> If you reply to this email, your message will be added to the discussion
>>> below:
>>>
>>> http://gromacs.5086.n6.nabble.com/How-to-can-i-replace-a-molecule-tp5001756p5001764.html
>>> To start a new topic under GROMACS Users Forum, email
>>> [hidden email]
>>> To unsubscribe from GROMACS, click here.
>>> NAML
>>
>>
>>
>
> --
> 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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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-- 
Best Regards,

Nur Syafiqah Abdul Ghani,
Theoretical and Computational Chemistry Laboratory,
Department of Chemistry,
Faculty of Science,
Universiti Putra Malaysia,
43400 Serdang,
Selangor.
013-7188131
alternative email : syafiqahabdulgh...@gmail.com




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Re: [gmx-users] how to center to molecule in pbc box?

[Carlos Javier Núñez]

Hi,

visualize your MD trajectory in VMD without water (or solvent) and without
ions (if have).
I hope this helps.

Regards,
Javier





2012/10/6 Albert 

> hello:
>
> I am using the following command for md production in gromacs:
>
> grompp -f md.mdp -p md.top -o md.tpr
>
> mpirun -np 64 mdrun -s md.tpr -x md.xtc -g md.log
>
> However, I found that the md.xtc file need command:
>
> trjconv -f md.xtc -o convert.xtc -pbc mol
>
> to put the molecule in the centre of pbc box, otherwise it is messy when
> we visualize in VMD. I am wondering, is it possible to ask mdrun generate
> the .xtc file cetering the molecule in PBC box automatically and we no
> longer need to use trjconv command to convert it.
>
> thank you very much
> best
> Albert
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