Re: [gmx-users] Force constant, regarding

[Dallas Warren]

Read the papers for the forcefield, that will tell you how things are
parameterised.

On Sat, 15 Sep. 2018, 2:49 am RAHUL SURESH,  wrote:

> Hi Users
>
> I am performing a simulation for a bonded metal-protein complex system.
> Here I am aware of adding the essential parameters in ffbonded .itp. The
> force constant value (kb) in the ffbonded.itp file is calculated using
> Gaussian. I would like to clarify the method I have adopted to measure kb
> value.
>
> Here the metal is bonded with three residues of a protein. I have isolated
> the metal-bonded residue and optimized using gaussian calculated the Kb
> value. Now in ffbonded.itp file, I have added Metal and residue atom bond
> length and  Kb value obtained from QM results, just like
> CU   O0.20134   507545.
>
> likewise, I have added all the bonds but kb remain the same.
>
> Regarding bond angle and dihedral, if the metal is bonded with oxygen of
> two histidines, what should be the nomenclature in naming atoms. Naming can
> be our choice or does it need to follow any protocol?
>
> How to calculate the cth value for the bond angle?
>
> How do we determine the coefficients of dihedral?
>
> Do I make the procedure complicated or can anyone suggest if any better
> methods?
>
> Sorry I have dumped the mail with too many questions.
>
> --
> *Regards,*
> *Rahul *
> --
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Re: [gmx-users] Error in NVT equilibration

[Dallas Warren]

As the warning indicates, due to the bond force constant and atom masses,
it will oscillate too fast for the time step. And as you found out, exactly
that happened and the system exploded. There are two ways that you can
"fix" that (reduce time step or bond force constant), but wouldn't
recommend either at this point. You need to look into the source of the
topology, how it was generated, why that force constant is applied to that
bond etc.

On Fri, 14 Sep. 2018, 11:06 pm Gonzalez Fernandez, Cristina, <
cristina.gonzalezf...@unican.es> wrote:

> Dear Gromacs users,
>
>
> I am trying to perform a nvt equilibration, but when I generate the .tpr
> file I get a warning indicating that a bond is oscillating too fast:
>
>
> The bond in molecule-type MOL_1 between atoms 38 C21 and 39 O22 has an
> estimated oscillational period of 2.4e-02 ps, which is less than 5 times
> the time step of 1.5e-02. Maybe you forgot to change the constraints mdp
> option.
>
>
>
> I have ignored it with the -maxwarn option and I obtain the .tpr file.
> However, when I run the simulation I obtain this error?
>
>
> Too many LINCS warnings (1630)
>
>
>
> Are the error and the warning related? How could I solve the Lincs error
> and the warning?
>
>
> I attach the .mdp file.
>
>
>
>
> Thank you in advance,
>
>
> C.
>
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[gmx-users] Regarding root mean square inner product from PCA

[vijayakumar gosu]

Dear Gromacs users,

I have done simulations of wild type and mutant proteins for 200ns. Further
for the backbone of the whole MD trajectory i have performed PCA analysis,
then calculated RMSIP for first 10 eigen vectors by using the wild-type and
mutant eigenvectors. When i look at the overlap of the variance, between WT
and mutant, third eigen vectors are identical. however when i checked for
the correlated motions along third eigen vector, using porcupine plot,  i
could see the difference in the direction of motion as well as in the
magnitude between WT and mutant.  (i have used -extr flag  to extract the
extreme conformation with 30 frames). I am bit confused to interpret the
result. any suggestions please.

Thanks in advance

Vijayakumar Gosu
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Re: [gmx-users] Make check failed 2018 Gromacs on GPU workstation

[Phuong Tran]

Thank you for your quick response.

I have no idea why the GPU unit test failed. The workstation was restarted,
so nothing was running at the time.  We have 1 Quadro 600, and 2 1080Ti on
it with CUDA 9.0.
Here is the result for the regression test:

Reading file topol.tpr, VERSION 2018.3 (single precision)

NOTE: Parallelization is limited by the small number of atoms,
  only starting 4 thread-MPI ranks.
  You can use the -nt and/or -ntmpi option to optimize the number of
threads.

Changing nstlist from 10 to 100, rlist from 1.4 to 1.536

Using 4 MPI threads
Using 8 OpenMP threads per tMPI thread


---
Program: gmx mdrun, version 2018.3
Source file: src/gromacs/taskassignment/taskassignment.cpp (line 251)
Function:std::vector >::value_type
gmx::runTaskAssignment(const std::vector&, const std::vector&,
const gmx_hw_info_t&, const gmx::MDLogger&, const t_commrec*, const
std::vector&)
MPI rank:0 (out of 4)

Inconsistency in user input:
There were 4 GPU tasks found on node ubuntuserver16, but 3 GPUs were
available. If the GPUs are equivalent, then it is usually best to have a
number of tasks that is a multiple of the number of GPUs. You should
reconsider your GPU task assignment, number of ranks, or your use of the
-nb,
-pme, and -npme options, perhaps after measuring the performance you can
get.

On Thu, Sep 13, 2018 at 4:11 PM Szilárd Páll  wrote:

> Test timeouts are strange, Is the machine you're running on busy with other
> jobs?
>
> Regarding the regressiontest failure, can you share
> tests/regressiontests*/complex/octahedron/mdrun.out
> please?
>
> --
> Szilárd
>
>
> On Thu, Sep 13, 2018 at 8:49 PM Phuong Tran 
> wrote:
>
> > Hi all,
> >
> > I have been trying to install Gromacs on our GPU workstation that has
> CUDA
> > 9.0
> > It went well but 'make check' have failed so far on either 2018.3 or
> 2018.2
> > versions.
> > anybody know how to resolve it?
> > Please see the error below.
> > Thank you,
> > -T
> >
> > Test project /home/user/Softwares/gromacs-2018.3/build
> >
> > .
> >
> >
> >  9/39 Test  #9: GpuUtilsUnitTests ***Timeout  30.35 sec
> >
> >
> > .
> >
> >
> > 35/39 Test #35: regressiontests/complex ..***Failed  174.98 sec
> >
> >
> >
> > GROMACS:  gmx mdrun, version 2018.3
> >
> > Executable:   /home/user/Softwares/gromacs-2018.3/build/bin/gmx
> >
> > Data prefix:  /home/user/Softwares/gromacs-2018.3 (source tree)
> >
> > Working dir:
> > /home/user/Softwares/gromacs-2018.3/build/tests/regressiontests-2018.3
> >
> > Command line:
> >
> >   gmx mdrun -h
> >
> >
> >
> > Thanx for Using GROMACS - Have a Nice Day
> >
> >
> > Mdrun cannot use the requested (or automatic) number of ranks, retrying
> > with 8.
> >
> >
> > Abnormal return value for ' gmx mdrun-nb cpu   -notunepme >mdrun.out
> > 2>&1' was 1
> >
> > Retrying mdrun with better settings...
> >
> >
> > Abnormal return value for ' gmx mdrun   -notunepme >mdrun.out 2>&1'
> was
> > -1
> >
> > FAILED. Check mdrun.out, md.log file(s) in octahedron for octahedron
> >
> > Re-running orientation-restraints using CPU-based PME
> >
> > Re-running pull_geometry_angle using CPU-based PME
> >
> > Re-running pull_geometry_angle-axis using CPU-based PME
> >
> > Re-running pull_geometry_dihedral using CPU-based PME
> >
> > 1 out of 55 complex tests FAILED
> >
> >
> >  
> >
> >
> > 95% tests passed, 2 tests failed out of 39
> >
> >
> > Label Time Summary:
> >
> > GTest  = 133.55 sec (33 tests)
> >
> > IntegrationTest=  88.38 sec (3 tests)
> >
> > MpiTest=   2.82 sec (3 tests)
> >
> > UnitTest   =  45.17 sec (30 tests)
> >
> >
> > Total Test time (real) = 810.78 sec
> >
> >
> > The following tests FAILED:
> >
> >   9 - GpuUtilsUnitTests (Timeout)
> >
> >  35 - regressiontests/complex (Failed)
> >
> > Errors while running CTest
> >
> > CMakeFiles/run-ctest-nophys.dir/build.make:57: recipe for target
> > 'CMakeFiles/run-ctest-nophys' failed
> >
> > make[3]: *** [CMakeFiles/run-ctest-nophys] Error 8
> >
> > CMakeFiles/Makefile2:1160: recipe for target
> > 'CMakeFiles/run-ctest-nophys.dir/all' failed
> >
> > make[2]: *** [CMakeFiles/run-ctest-nophys.dir/all] Error 2
> >
> > CMakeFiles/Makefile2:971: recipe for target 'CMakeFiles/check.dir/rule'
> > failed
> >
> > make[1]: *** [CMakeFiles/check.dir/rule] Error 2
> >
> > Makefile:546: recipe for target 'check' failed
> >
> > make: *** [check] Error 2
> > ReplyForward
> > 
> > 
> > 
> > 
> > --
> > Gromacs Users mailing list
> >
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> > posting!
> >
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> >
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> > https:

[gmx-users] (no subject)

[SAKO MIRZAIE]

Hi every one,
I need the topology parameters for pyridoxal phosphate linked to lysine
with amber99sb force field. does anyone have the mentioned parameters? I
searched it among publications but I didn't find it at all.

Best regards,

-- 
***
Sako Mirzaie
Ph.D. in biochemistry, Assistant Professor, Science Faculty, Islamic Azad
University of Sanandaj, Sanandaj, Iran

http://www.iausdj.ac.ir/_Academician?username=sakomirzaie

http://www.iausdj.ac.ir/_Academician/English?username=sakomirzaie

http://scholar.google.com/citations?user=viwZvVAJ&hl=en

http://www.scopus.com/authid/detail.url?authorId=54886431500

http://www.ncbi.nlm.nih.gov/pubmed/?term=sako+mirzaie
https://www.researchgate.net/profile/Sako_Mirzaie/publications/
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[gmx-users] Force constant, regarding

[RAHUL SURESH]

Hi Users

I am performing a simulation for a bonded metal-protein complex system.
Here I am aware of adding the essential parameters in ffbonded .itp. The
force constant value (kb) in the ffbonded.itp file is calculated using
Gaussian. I would like to clarify the method I have adopted to measure kb
value.

Here the metal is bonded with three residues of a protein. I have isolated
the metal-bonded residue and optimized using gaussian calculated the Kb
value. Now in ffbonded.itp file, I have added Metal and residue atom bond
length and  Kb value obtained from QM results, just like
CU   O0.20134   507545.

likewise, I have added all the bonds but kb remain the same.

Regarding bond angle and dihedral, if the metal is bonded with oxygen of
two histidines, what should be the nomenclature in naming atoms. Naming can
be our choice or does it need to follow any protocol?

How to calculate the cth value for the bond angle?

How do we determine the coefficients of dihedral?

Do I make the procedure complicated or can anyone suggest if any better
methods?

Sorry I have dumped the mail with too many questions.

-- 
*Regards,*
*Rahul *
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[gmx-users] bromide/iodide parameters for charm36

[Carlos Navarro]

Dear all,
Currently, I'm looking for bromide/iodide parameters for charmm36 without
luck.
Does anyone know where I can find them?
Best regards and thanks in advance,
Carlos

--

Carlos Navarro Retamal

Bioinformatic Engineering. PhD

Postdoctoral Researcher in Center for Bioinformatics and Molecular
Simulations

Universidad de Talca

Av. Lircay S/N, Talca, Chile

T: (+56) 712201  798

E: carlos.navarr...@gmail.com or cnava...@utalca.cl
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[gmx-users] GBSA parameters

[Jack Shepherd]

Dear all,

I am interested in running an implicit solvent DNA simulation. Attempting
to run grompp with gbsa turned on resulted in the error message

GB parameter(s) missing or negative for atom type 'OS'

GB parameter(s) missing or negative for atom type 'H2'

GB parameter(s) missing or negative for atom type 'N*'

GB parameter(s) missing or negative for atom type 'CK'

GB parameter(s) missing or negative for atom type 'P'

---
Program: gmx grompp, version 2018.2
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 1335)

Fatal error:
Can't do GB electrostatics; the implicit_genborn_params section of the
forcefield is missing parameters for 5 atomtypes or they might be negative.

The PDB was generated with nab from AmberTools 16.

Clearly I need to add the GBSA values to /usr/share/./gbsa.itp. My
guess is that I can copy the hydrogen values from the other hydrogens as
they are all the same, and choose an appropriate line to copy for the O,
N*, and CK.

Can anyone point to something which will help me with which to copy and how
to add the missing P values? Or a download I may have missed somewhere
along the way?

Thanks all in advance

jack
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[gmx-users] Error in NVT equilibration

[Gonzalez Fernandez, Cristina]

Dear Gromacs users,


I am trying to perform a nvt equilibration, but when I generate the .tpr file I 
get a warning indicating that a bond is oscillating too fast:


The bond in molecule-type MOL_1 between atoms 38 C21 and 39 O22 has an 
estimated oscillational period of 2.4e-02 ps, which is less than 5 times the 
time step of 1.5e-02. Maybe you forgot to change the constraints mdp option.



I have ignored it with the -maxwarn option and I obtain the .tpr file. However, 
when I run the simulation I obtain this error?


Too many LINCS warnings (1630)



Are the error and the warning related? How could I solve the Lincs error and 
the warning?


I attach the .mdp file.




Thank you in advance,


C.

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Re: [gmx-users] (no subject)

[AKANXA TIWARI]

thanks for reply


On Fri, Sep 14, 2018 at 5:09 PM Justin Lemkul  wrote:

>
>
> On 9/14/18 6:48 AM, AKANXA TIWARI wrote:
> > i am getting a warning after converting pdb2gmx and then applying force
> > field what i will do. please help me.i get this on screen.
> > WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was
> > mapped
> > to an entry in the topology database, but the atom H used in
> > an interaction of type angle in that entry is not found in the
> > input file. Perhaps your atom and/or residue naming needs to be
> > fixed.
> >
> >
> >
> > WARNING: WARNING: Residue 374 named PHE of a molecule in the input file
> was
> > mapped
> > to an entry in the topology database, but the atom O used in
> > an interaction of type angle in that entry is not found in the
> > input file. Perhaps your atom and/or residue naming needs to be
> > fixed.
> >
>
> pdb2gmx is just being a bit too noisy here. Termini are being patched,
> which means some atoms get deleted, replaced, or added. Here, an
> existing atom is being deleted and replaced with another at both the N-
> and C-termini. There is no problem, as you see the message below about
> successful completion.
>
> -Justin
>
> > Before cleaning: 6050 pairs
> > Before cleaning: 7868 dihedrals
> > Making cmap torsions...
> > There are 2709 dihedrals, 1833 impropers, 5404 angles
> >6050 pairs, 3705 bonds and 0 virtual sites
> > Total mass 40604.576 a.m.u.
> > Total charge 11.000 e
> > Writing topology
> >
> > Back Off! I just backed up posre.itp to ./#posre.itp.1#
> >
> > Writing coordinate file...
> >
> > Back Off! I just backed up actin_asp_processed.gro to
> > ./#actin_asp_processed.gro.1#
> >  - PLEASE NOTE 
> > You have successfully generated a topology from: actin_asp_clean.pdb.
> > The Gromos54a7 force field and the spce water model are used.
> >  - ETON ESAELP 
> >
> > GROMACS reminds you: "Miggida-Miggida-Miggida-Mac" (Kriss Kross)
> >
> > akanxa@akanxa-HP-Notebook:~/Documents/aasp$
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
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Re: [gmx-users] Justin paper 2010 pulling

[Justin Lemkul]

On 9/14/18 3:14 AM, Rakesh Mishra wrote:

Dear Dr. Justin,

Of course I agree with your points. There is no point to not believe on you,
that's why we are discussing and thanks for your comment.
I raised the question because I observed the problem .
And it was matter of just common sense for me that
why the change of saving frequency is affecting the much difference
in the maximum value of force curve in pulling along the axial direction.

Let me clear again, I say Input parameters of the pull.mdp files are same
for both the simulation.
Only difference is the different saving frequency of position and energy
coordinates.
Please see below two cases

Case -A

   simulation of same system with same input parameter during pulling
1  nstxtcout= 2000   ; every 4 ps
 nstenergy= 5000

2  nstxtcout= 2000   ; every 4 ps
 nstenergy= 2000

(output files, pullf1.xvg, and pullf2.xvg are different very much w.r.t
peak value of force )
 Same thing happening also in the following below case, please see
this.

Case B.

1  nstxtcout= 2000   ; every 4 ps
 nstenergy   = 5000

2-  nstxtcout= 1000   ; every 4 ps
  nstenergy   = 5000

Because, now this gromacs discussion user platform do not allow to upload
any other data (eg, plot, pdf file etc) otherwise I can upload the plot.


You can always upload images to file-sharing services and provide links.

But first, watch the trajectories and see how they're behaving. The 
systems are likely just doing somewhat different things, as I said 
before. There is no reason to expect even the exact same .tpr file to 
produce the exact same output (binary identical), for reasons stated 
here: http://www.gromacs.org/Documentation/Terminology/Reproducibility


Again, I emphasize that output control has no impact on the computation 
of forces or anything to do with the pull code. This cannot be the 
reason for differences in trajectories.


-Justin


On Thu, Sep 13, 2018 at 4:57 PM, Justin Lemkul  wrote:



On 9/13/18 1:20 AM, Rakesh Mishra wrote:


I do not believe .

Because if I run multiple simulation of pulling with the same system and
with the
same inputs then almost we are getting similar force/time curve.
While we are getting different curve if we are saving position coordinates
or energy
coordinates with different frequency.


There is no aspect of the code in which the computation of forces depends
on output frequency. You're welcome to disbelieve me, but you're clearly
just getting different simulation outcomes from different inputs, or
there's something else that differs that you haven't realized or haven't
told us.

-Justin


On Wed, Sep 12, 2018 at 8:15 PM, Justin Lemkul  wrote:



On 9/12/18 8:42 AM, Rakesh Mishra wrote:

Dear Justin

It is totally surprised for me.
I am pulling the same system of bdna
with the same constant velocity (0.005nm/ps).

Case 1
let for first case, When I am saving position coordinate (nstxtc ) in
the
interval of 4ps
and saving energy coordinate in the interval of 4ps.

Case 2
In the second case of pulling of the same system with the same velocity,
we
save position
coordinate in the interval of 4ps but we save energy coordinate in the
interval of  10ps.

Now in the output file of force.xvg for both case qualitative behaviour
of
diagram is same but
Peak of the forces are much differ.  Why this saving frequency is
affecting
the peak value. While
it is just saving the coordinates.

We also found that, if we save energy coordinate with the same frequency
and position
coordinate with different frequency then, again peak value of forces are
different.
Which should not. Why it is happening. Can you clarify please.

Your results have nothing to do with the save frequency. The output in

pullf.xvg is specified by pull-nstfout, not any of the others. You have
different simulations that behave differently, because there are elements
of randomness in any MD simulation. Pulling is a non-equilibrium process;
you may have to run several times with different pull vectors to find the
minimum-energy path.

-Justin



On Thu, Sep 6, 2018 at 5:20 PM, Justin Lemkul  wrote:


On 9/6/18 2:29 AM, Rakesh Mishra wrote:

While I have purely physics background.


But, In my thinking, there are hydrogen bonds (electrostatic
attractive
interaction)
between bp of  both the strands of DNA/RNA  which are perpendicular to
helix direction.
And the other thing you have chosen very fast velocity like (0.01,
0.001,
0.005 ).
This can also be the reason of smoothness. But can you tell me one
thing
please,the
value of spring constant of biasing that you have taken (k= 1000), is
standard or not . If this value can be taken for peptide pulling .
Can
this value of
spring constant (k=1000) can be taken  for DNA (or dna+drug) pulling
or
not .

There is no such thing as a "standard" force cons
tant
for pulling.


-Justin

--
==

Re: [gmx-users] (no subject)

[Justin Lemkul]

On 9/14/18 6:48 AM, AKANXA TIWARI wrote:

i am getting a warning after converting pdb2gmx and then applying force
field what i will do. please help me.i get this on screen.
WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was
mapped
to an entry in the topology database, but the atom H used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.



WARNING: WARNING: Residue 374 named PHE of a molecule in the input file was
mapped
to an entry in the topology database, but the atom O used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.



pdb2gmx is just being a bit too noisy here. Termini are being patched, 
which means some atoms get deleted, replaced, or added. Here, an 
existing atom is being deleted and replaced with another at both the N- 
and C-termini. There is no problem, as you see the message below about 
successful completion.


-Justin


Before cleaning: 6050 pairs
Before cleaning: 7868 dihedrals
Making cmap torsions...
There are 2709 dihedrals, 1833 impropers, 5404 angles
   6050 pairs, 3705 bonds and 0 virtual sites
Total mass 40604.576 a.m.u.
Total charge 11.000 e
Writing topology

Back Off! I just backed up posre.itp to ./#posre.itp.1#

Writing coordinate file...

Back Off! I just backed up actin_asp_processed.gro to
./#actin_asp_processed.gro.1#
 - PLEASE NOTE 
You have successfully generated a topology from: actin_asp_clean.pdb.
The Gromos54a7 force field and the spce water model are used.
 - ETON ESAELP 

GROMACS reminds you: "Miggida-Miggida-Miggida-Mac" (Kriss Kross)

akanxa@akanxa-HP-Notebook:~/Documents/aasp$


--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] (no subject)

[Bratin Kumar Das]

You need to add the particular H to the amino acid .rtp file in the
forcefield folder

On Fri, Sep 14, 2018, 4:24 PM AKANXA TIWARI 
wrote:

> i am getting a warning after converting pdb2gmx and then applying force
> field what i will do. please help me.i get this on screen.
> WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was
> mapped
> to an entry in the topology database, but the atom H used in
> an interaction of type angle in that entry is not found in the
> input file. Perhaps your atom and/or residue naming needs to be
> fixed.
>
>
>
> WARNING: WARNING: Residue 374 named PHE of a molecule in the input file was
> mapped
> to an entry in the topology database, but the atom O used in
> an interaction of type angle in that entry is not found in the
> input file. Perhaps your atom and/or residue naming needs to be
> fixed.
>
>
> Before cleaning: 6050 pairs
> Before cleaning: 7868 dihedrals
> Making cmap torsions...
> There are 2709 dihedrals, 1833 impropers, 5404 angles
>   6050 pairs, 3705 bonds and 0 virtual sites
> Total mass 40604.576 a.m.u.
> Total charge 11.000 e
> Writing topology
>
> Back Off! I just backed up posre.itp to ./#posre.itp.1#
>
> Writing coordinate file...
>
> Back Off! I just backed up actin_asp_processed.gro to
> ./#actin_asp_processed.gro.1#
> - PLEASE NOTE 
> You have successfully generated a topology from: actin_asp_clean.pdb.
> The Gromos54a7 force field and the spce water model are used.
> - ETON ESAELP 
>
> GROMACS reminds you: "Miggida-Miggida-Miggida-Mac" (Kriss Kross)
>
> akanxa@akanxa-HP-Notebook:~/Documents/aasp$
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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[gmx-users] (no subject)

[AKANXA TIWARI]

i am getting a warning after converting pdb2gmx and then applying force
field what i will do. please help me.i get this on screen.
WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was
mapped
to an entry in the topology database, but the atom H used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.



WARNING: WARNING: Residue 374 named PHE of a molecule in the input file was
mapped
to an entry in the topology database, but the atom O used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.


Before cleaning: 6050 pairs
Before cleaning: 7868 dihedrals
Making cmap torsions...
There are 2709 dihedrals, 1833 impropers, 5404 angles
  6050 pairs, 3705 bonds and 0 virtual sites
Total mass 40604.576 a.m.u.
Total charge 11.000 e
Writing topology

Back Off! I just backed up posre.itp to ./#posre.itp.1#

Writing coordinate file...

Back Off! I just backed up actin_asp_processed.gro to
./#actin_asp_processed.gro.1#
- PLEASE NOTE 
You have successfully generated a topology from: actin_asp_clean.pdb.
The Gromos54a7 force field and the spce water model are used.
- ETON ESAELP 

GROMACS reminds you: "Miggida-Miggida-Miggida-Mac" (Kriss Kross)

akanxa@akanxa-HP-Notebook:~/Documents/aasp$
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Re: [gmx-users] Tolerance and damping coefficient

[Gonzalez Fernandez, Cristina]

Thank you Justin


De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 en nombre de Justin Lemkul 

Enviado: martes, 11 de septiembre de 2018 18:02:51
Para: gmx-us...@gromacs.org
Asunto: Re: [gmx-users] Tolerance and damping coefficient



On 9/11/18 11:09 AM, Gonzalez Fernandez, Cristina wrote:
> Dear Gromacs users,
>
>
> I am trying to reproduce the simulation of a published article and in it the 
> authors used Particle Meah Ewald for electrostatic interactions with a 
> relative tolerance of 10^⁻6. I have checked the manual and I only have found 
> tolerance parameters for energy minimization, neighbour searching and shake 
> algorithm. Does anyone know how to implement the tolerance for PME?. On the 
> other hand, in the paper Langevin dynamics for temperature and piston

See "ewald-rtol"
(http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#ewald)

> fluctuations are considered, with a damping coefficient of 1 ps^-1. However, 
> in the Gromacs manual Langevin dynamics only includes bd-fric and ld-seed, 
> whose units differ from ps^⁻1. How can I consider the damping coefficent?

That's tau-t when the integrator is sd (see entry for "sd" in
http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#run-control)

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] Justin paper 2010 pulling

[Rakesh Mishra]

Dear Dr. Justin,

Of course I agree with your points. There is no point to not believe on you,
that's why we are discussing and thanks for your comment.
I raised the question because I observed the problem .
And it was matter of just common sense for me that
why the change of saving frequency is affecting the much difference
in the maximum value of force curve in pulling along the axial direction.

Let me clear again, I say Input parameters of the pull.mdp files are same
for both the simulation.
Only difference is the different saving frequency of position and energy
coordinates.
Please see below two cases

Case -A

  simulation of same system with same input parameter during pulling
1  nstxtcout= 2000   ; every 4 ps
nstenergy= 5000

2  nstxtcout= 2000   ; every 4 ps
nstenergy= 2000

   (output files, pullf1.xvg, and pullf2.xvg are different very much w.r.t
peak value of force )
Same thing happening also in the following below case, please see
this.

Case B.

1  nstxtcout= 2000   ; every 4 ps
nstenergy   = 5000

2-  nstxtcout= 1000   ; every 4 ps
 nstenergy   = 5000

Because, now this gromacs discussion user platform do not allow to upload
any other data (eg, plot, pdf file etc) otherwise I can upload the plot.

On Thu, Sep 13, 2018 at 4:57 PM, Justin Lemkul  wrote:

>
>
> On 9/13/18 1:20 AM, Rakesh Mishra wrote:
>
>> I do not believe .
>>
>> Because if I run multiple simulation of pulling with the same system and
>> with the
>> same inputs then almost we are getting similar force/time curve.
>> While we are getting different curve if we are saving position coordinates
>> or energy
>> coordinates with different frequency.
>>
>
> There is no aspect of the code in which the computation of forces depends
> on output frequency. You're welcome to disbelieve me, but you're clearly
> just getting different simulation outcomes from different inputs, or
> there's something else that differs that you haven't realized or haven't
> told us.
>
> -Justin
>
>
> On Wed, Sep 12, 2018 at 8:15 PM, Justin Lemkul  wrote:
>>
>>
>>> On 9/12/18 8:42 AM, Rakesh Mishra wrote:
>>>
>>> Dear Justin

 It is totally surprised for me.
I am pulling the same system of bdna
 with the same constant velocity (0.005nm/ps).

 Case 1
 let for first case, When I am saving position coordinate (nstxtc ) in
 the
 interval of 4ps
 and saving energy coordinate in the interval of 4ps.

 Case 2
 In the second case of pulling of the same system with the same velocity,
 we
 save position
 coordinate in the interval of 4ps but we save energy coordinate in the
 interval of  10ps.

 Now in the output file of force.xvg for both case qualitative behaviour
 of
 diagram is same but
 Peak of the forces are much differ.  Why this saving frequency is
 affecting
 the peak value. While
 it is just saving the coordinates.

 We also found that, if we save energy coordinate with the same frequency
 and position
 coordinate with different frequency then, again peak value of forces are
 different.
 Which should not. Why it is happening. Can you clarify please.

 Your results have nothing to do with the save frequency. The output in
>>> pullf.xvg is specified by pull-nstfout, not any of the others. You have
>>> different simulations that behave differently, because there are elements
>>> of randomness in any MD simulation. Pulling is a non-equilibrium process;
>>> you may have to run several times with different pull vectors to find the
>>> minimum-energy path.
>>>
>>> -Justin
>>>
>>>
>>>
>>> On Thu, Sep 6, 2018 at 5:20 PM, Justin Lemkul  wrote:


 On 9/6/18 2:29 AM, Rakesh Mishra wrote:
>
> While I have purely physics background.
>
>> But, In my thinking, there are hydrogen bonds (electrostatic
>> attractive
>> interaction)
>> between bp of  both the strands of DNA/RNA  which are perpendicular to
>> helix direction.
>> And the other thing you have chosen very fast velocity like (0.01,
>> 0.001,
>> 0.005 ).
>> This can also be the reason of smoothness. But can you tell me one
>> thing
>> please,the
>> value of spring constant of biasing that you have taken (k= 1000), is
>> standard or not . If this value can be taken for peptide pulling .
>> Can
>> this value of
>> spring constant (k=1000) can be taken  for DNA (or dna+drug) pulling
>> or
>> not .
>>
>> There is no such thing as a "standard" force cons
>> tant
>> for pulling.
>>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
>>