from:"Vytautas Rakeviius"

 4 days after original post without answer at all I think every post is helpful 
somewhat. Especially when it encourages discussion and even more answers right 
away. 
Am I wrong?

On Monday, September 17, 2018, 4:48:52 PM GMT+3, João Henriques 
 wrote:  

 I'm sure there's lots of software that can perform that task, I just felt
it was important to underline that a kernel density estimation is what is
needed in this case. If you go back to your original reply, there's nothing
in there that can help the original poster solving his problem.

J

On Mon, Sep 17, 2018 at 3:43 PM Vytautas Rakeviius 
wrote:

>  Also you can use R for that task. Very easy like:density(x, ...)
>
>    On Monday, September 17, 2018, 4:26:38 PM GMT+3, João Henriques <
> joao.m.a.henriq...@gmail.com> wrote:
>
>  How does that reply the OP's question? To calculate the joint probability
> distribution you need to perform a kernel density estimation. I'd recommend
> either SciPy or Seaborn if you're not averse to coding in Python:
>
>
> https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.gaussian_kde.html
> https://seaborn.pydata.org/examples/joint_kde.html
>
> With Seaborn this is an incredibly simple task.
>
> J
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Re: [gmx-users] Population Density Plot

 Also you can use R for that task. Very easy like:density(x, ...)

On Monday, September 17, 2018, 4:26:38 PM GMT+3, João Henriques 
 wrote:  
 
 How does that reply the OP's question? To calculate the joint probability
distribution you need to perform a kernel density estimation. I'd recommend
either SciPy or Seaborn if you're not averse to coding in Python:

https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.gaussian_kde.html
https://seaborn.pydata.org/examples/joint_kde.html

With Seaborn this is an incredibly simple task.

J
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Re: [gmx-users] Population Density Plot

 Gromacs xvg files can be opened with Xmgrace and you should get plot out of 
them right away then. I am not sure that those plots fit your need but you can 
edit them with same program right away.Xmgrace is probably available over your 
Linux distribution package manager like "sudo apt-get install grace" command on 
Ubuntu and Debian.

On Thursday, September 13, 2018, 4:57:17 PM GMT+3, ISHRAT JAHAN 
 wrote:  
 
 Dear all,
Can anyone tell me the command used for calculating the population density
plot between Ree and Rg? As I have calculated the Ree and Rg value from gmx
polystat command now, i want to plot population density between Ree and Rg.
Your help will be appreciated.
Thank u
-
Ishrat Jahan
Research Scholar
Department Of Chemistry
A.M.U Aligarh
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Re: [gmx-users] Error in NVT equilibration

 And what about OPLS-AA/L if I do nvt equilibration of my protein in water with 
it is it OK to do constraints   = all-bondsall the time like I am 
used to do?

On Monday, September 17, 2018, 3:18:51 PM GMT+3, Justin Lemkul 
 wrote:  

On 9/17/18 8:12 AM, Vytautas Rakeviius wrote:
> Can you explain more to us when it is not appropriate to constrain all bonds 
> during nvt equilibration?

The use of constraints is not tied to the statistical mechanical 
ensemble or the simulation process (equilibration, production, etc). 
Constraints are a convention of force fields. For example, it is stated 
in the primary literature for the GROMOS force fields that all bonds are 
constrained. That is an assumption within the physical model, and proper 
use of that force field dictates that the user should follow that 
convention. For CHARMM, only bonds to H are to be constrained, because 
the bond vibrations are expected to be present. Every intramolecular 
interaction is linked - if you violate the force field convention with 
respect to bonds, then the angle vibrations are inconsistent with the 
parametrization, the dihedrals (which are tied to both bonds and angles) 
are not necessarily employed correctly, etc.

The main point: every element of a force field, from its cutoffs, water 
model, use of constraints, etc. is linked. While there are deviations 
from this "absolute" statement in certain cases, consider this a pretty 
strong rule for doing accurate and reliable simulations. There are not 
as many choices to be made as one might expect.

-Justin

>    On Monday, September 17, 2018, 3:06:56 PM GMT+3, Justin Lemkul 
> wrote:
>  
>  
>
> On 9/17/18 8:04 AM, Vytautas Rakeviius wrote:
>>    I think your attachment to email was lost during re-transfer and it would 
>>be nice to see that, but I think what you need is:constraints                
>>= all-bondsIn that mdp file.
> That depends on the force field convention. It is not universally
> appropriate to constrain all bonds (and certainly should not be the
> "solution" to just "make the warning go away"), and the warning from
> grompp may not actually be the source of any problem.
>
> -Justin
>
>>        On Friday, September 14, 2018, 4:07:43 PM GMT+3, Gonzalez Fernandez, 
>>Cristina  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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Assistant Professor
Virginia Tech Department of Biochemistry

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

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Re: [gmx-users] Error in NVT equilibration

Can you explain more to us when it is not appropriate to constrain all bonds 
during nvt equilibration?
   On Monday, September 17, 2018, 3:06:56 PM GMT+3, Justin Lemkul 
 wrote:  

On 9/17/18 8:04 AM, Vytautas Rakeviius wrote:
>  I think your attachment to email was lost during re-transfer and it would be 
>nice to see that, but I think what you need is:constraints                = 
>all-bondsIn that mdp file.

That depends on the force field convention. It is not universally 
appropriate to constrain all bonds (and certainly should not be the 
"solution" to just "make the warning go away"), and the warning from 
grompp may not actually be the source of any problem.

-Justin

>      On Friday, September 14, 2018, 4:07:43 PM GMT+3, Gonzalez Fernandez, 
>Cristina  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.

-- 
==

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] Error in NVT equilibration

 I think your attachment to email was lost during re-transfer and it would be 
nice to see that, but I think what you need is:constraints= 
all-bondsIn that mdp file.

On Friday, September 14, 2018, 4:07:43 PM GMT+3, Gonzalez Fernandez, 
Cristina  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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Re: [gmx-users] Regarding index .ndx files

 Without going into details and setting:
tc-grps = System 
should allow to proceed without fatal errors.
On Monday, September 17, 2018, 1:58:50 PM GMT+3, Sebastian Muraru 
 wrote:  
 
 Hi there! I am a Masters student and this is my first email to the list. I 
would just like to ask whether someone can clarify something for me regarding 
the index .ndx files.
I am using an nvt.mdp file in order to run an nvt equilibration step. The 
section of interest is the following (currently receiving an error):

###
; Temperature coupling is on
tcoupl          = V-rescale                ; modified Berendsen thermostat
tc-grps        = CX ssdna; 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
###

The current error says that a number of atoms are not part of any of the 
T-Coupling groups. Therefore I have the following questions:
- Does this mean all atoms (including SOL) must be included in the groups 
specified using 'tc-grps'?
- If my index.ndx file is very large (contains > 20 groups), do I have to 
manually write them down at 'tc-grps' in the mdp file or is there a way to 
automatically import the groups present in the index.ndx file?

Best,
Sebastian
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Re: [gmx-users] (no subject)

 I suggest this tool:https://github.com/llazzaro/acpype 

On Friday, September 14, 2018, 10:44:56 PM GMT+3, SAKO MIRZAIE 
 wrote:  
 
 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=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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Re: [gmx-users] lie calculations

2018-09-13 Thread Vytautas Rakeviius

 Hi I think you should check this paper:Åqvist J, Medina C, Samuelsson JE. A 
new method for predicting binding affinity in computer-aided drug design. 
Protein Engineering, Design and Selection. 1994 Mar 1;7(3):385-91.It explains 
everything and gives example of use.And yes with different water models you 
should expect more or less different results.
Also as you see those fitting coefficients in paper like 0.5 or alpha or beta 
etc. I suggest refitting with your own data-set water model force field etc. as 
those numbers depend on such things. That became clear far later after this 
original paper.
On Wednesday, September 12, 2018, 6:35:23 PM GMT+3, Graham Jackson 
 wrote:  
 
 Hi All
I have looked at the manual and can execute LIE but I want to understand the 
process.  The manual gives instructions but no background theory. The theory I 
have seen does not explain how GROMACS does the calculation.  I have a 
simulation of a ligand bound to a receptor embedded in a POPC membrane.  I also 
have a simulation of the ligand in water.  I use these two for the lie 
calculation.  Is this correct and does the choice of water (spc TIP3P Tip4P) 
matter?

Thanks
Graham



—
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Department of Chemistry
University of Cape Town
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Re: [gmx-users] charmm2gromacs.py

2018-09-12 Thread Vytautas Rakeviius

 I never tried that myself, but I think you such check this:J. Chem. Inf. 
Model., 2016, 56 (6), pp 1112–1116DOI: 10.1021/acs.jcim.6b00103

On Wednesday, September 12, 2018, 11:19:44 AM GMT+3, Frederic Schneider 
 wrote:  
 
 Hi,

i use the parameter generator for organic molecules at paramchem.org and 
i am very thankful, that it was updated for the use of CGenFF 4.0. Now 
there is a problem with converting the .str file to gromacs topology 
files. I think, that the python script hosted  on the homepage of the 
MacKerell Lab does not support the lone pairs which are included since 
4.0.  Does anyone know, if there are a newer version of the script?

Thanks!

Best regards

Frederic


-- 
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TU Braunschweig
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Pharmazeutische Chemie
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Re: [gmx-users] core-dumped

2018-09-12 Thread Vytautas Rakeviius

 Investigate atoms 18720 and 18723 mentioned in error. From my experience such 
error happens when two atoms collide in completely unrealistic fashion.This 
error also dumps some pdb files at exact moment when things went really wrong 
and that ones you should look at.
Also I do not know what kind of settings file you used for minimization, but 
this one is my favorite: 
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/Files/minim.mdp
You should try it.

On Tuesday, September 11, 2018, 7:33:25 AM GMT+3, Bratin Kumar Das 
<177cy500.bra...@nitk.edu.in> wrote:  
 
 Dear all,
            During nvt equilibration I am getting the following error
gmx mdrun -v -s npt.tpr -deffnm npt
                      :-) GROMACS - gmx mdrun, 2016.5 (-:

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Bjelkmar
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 Christoph Junghans  Anca Hamuraru    Vincent Hindriksen Dimitrios
Karkoulis
    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson
  Justin A. Lemkul  Magnus Lundborg  Pieter Meulenhoff    Erik Marklund
  Teemu Murtola      Szilard Pall      Sander Pronk      Roland Schulz
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Copyright (c) 2001-2017, The GROMACS development team at
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check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
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as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:      gmx mdrun, version 2016.5
Executable:  /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Working dir:
/home/workstation/Documents/GROMACS_projects/GROMACS_GCGR_GLUCAGON_2
Command line:
  gmx mdrun -v -s npt.tpr -deffnm npt


Running on 1 node with total 4 cores, 4 logical cores
Hardware detected:
  CPU info:
    Vendor: Intel
    Brand:  Intel(R) Xeon(R) CPU E3-1225 v5 @ 3.30GHz
    SIMD instructions most likely to fit this hardware: AVX2_256
    SIMD instructions selected at GROMACS compile time: AVX2_256

  Hardware topology: Basic

Reading file npt.tpr, VERSION 2016.5 (single precision)
Changing nstlist from 5 to 25, rlist from 1.2 to 1.233

Using 1 MPI thread
Using 4 OpenMP threads


WARNING: This run will generate roughly 6779 Mb of data

starting mdrun '5YQZ_preprocessed - hbond-opt in water'
20 steps,    400.0 ps.

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 7.344571, max 575.613892 (between atoms 18720 and 18723)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  2379  2380  37.5    0.0872  0.1066      0.1010
  2381  2382  47.9    0.1498  0.1052      0.1090
  2383  2384  47.4    0.0884  0.1147      0.1090
  2389  2390  49.1    0.0597  0.1001      0.0960
  2426  2427  90.0    0.1253  0.1266      0.1080
  4036  4037  54.9    0.1454  0.1077      0.1090
  4038  4039  46.1    0.1081  0.1121      0.1090
  4040  4041  30.2    0.0554  0.1124      0.1090
  4040  4042  32.8    0.1002  0.1123      0.1090
  4040  4043  35.1    0.1426  0.1129      0.1090
  5382  5384  50.3    0.1280  0.1093      0.1090
  5956  5957  37.0    0.0770  0.1141      0.1090
  5956  5959  89.8    0.1805  0.1828      0.1090
  5960  5961  61.7    0.1651  0.1267      0.1229
  6029  6031  89.9    0.1146  1.2008      0.1090
  6035  6036  31.6    0.1083  0.1036      0.1010
  6038  6040  42.5    0.1324  0.1043      0.1010
  6887  6888  31.1    0.1070  0.      0.1090
  6887  6889  59.5    0.1351  0.1100      0.1090
  13006  13007  42.3    0.1575  0.1385      0.1610
  13007  13008  41.7    0.1436  0.1329      0.1480
  13007  13009  90.0    0.1348  0.2201      0.1480
  13007  13010  38.2    0.1530  0.1563      0.1610
  18672  18673  86.0    0.1515  0.2646      0.1530
  18673  18674  92.0    0.1407  1.1474      0.1430
  18674  18675  124.6    0.1445  23.3042      0.1610
  18675  18677  82.6    0.1723  23.9350      0.1480
  18675  18678  106.9    0.1522  23.6614      0.1610
  18678  18679  89.6    0.1402  0.9389      0.1430
  18679  18680  92.0    0.1552  0.1875      0.1530
  18723  18724  62.7    0.1687  73.2199      0.1470
  18724  18725  89.5    0.1607  0.8262      0.1530
  18725  18726  90.8    0.1420  0.1872      0.1430
  18720  18723  156.7    0.1620  84.7622      0.1470
  18721  18723  66.7    0.1602  72.9378      0.1470
  18722  18723  67.9    0.1335  72.8562      0.1470
  20543  20544  88.9    0.1496  0.1505      0.1470

Re: [gmx-users] Help

2018-07-11 Thread Vytautas Rakeviius

 https://www.urbandictionary.com/define.php?term=btw :) He wants you to try 
never version 2018.2:
ftp://ftp.gromacs.org/pub/gromacs/gromacs-2018.2.tar.gz
Also try different fftw options.
On cmake line add:
-DGMX_FFT_LIBRARY=xxx
where xxx can be fftw, mkl or fftpack. You also need proper stuff installed on 
our system for some of those options others will cause slow downs.



On Wednesday, July 11, 2018, 3:13:57 PM GMT+3, Maximiliano Sebastián 
Castillo  wrote:  
 
 Sorry, but... what is BTW 2018.2? Another software?

El mié., 11 jul. 2018 a las 6:50, Mark Abraham ()
escribió:

> Hi,
>
> I haven't seen that, and don't know how to guess what might make it work.
> BTW 2018.2 is a better idea to install.
>
> Mark
>
> On Wed, Jul 11, 2018 at 3:34 AM Maximiliano Sebastián Castillo <
> mcasti...@itba.edu.ar> wrote:
>
> > Hello,
> > I have the next problem:
> > [  1%] No patch step for 'fftwBuild'
> > [  1%] No update step for 'fftwBuild'
> > [  1%] Performing configure step for 'fftwBuild'
> > checking for a BSD-compatible install... /usr/bin/install -c
> > checking whether build environment is sane... configure: error: unsafe
> > srcdir value: '/home/maximiliano/Proyecto
> > Final/gromacs-2018/build/src/contrib/fftw/fftwBuild-prefix/src/fftwBuild'
> > src/contrib/fftw/CMakeFiles/fftwBuild.dir/build.make:109: recipe for
> target
> >
> 'src/contrib/fftw/fftwBuild-prefix/src/fftwBuild-stamp/fftwBuild-configure'
> > failed
> > make[2]: ***
> >
> [src/contrib/fftw/fftwBuild-prefix/src/fftwBuild-stamp/fftwBuild-configure]
> > Error 1
> > CMakeFiles/Makefile2:1440: recipe for target
> > 'src/contrib/fftw/CMakeFiles/fftwBuild.dir/all' failed
> > make[1]: *** [src/contrib/fftw/CMakeFiles/fftwBuild.dir/all] Error 2
> > Makefile:162: recipe for target 'all' failed
> > make: *** [all] Error 2
> >
> >
> > What can I do for it?
> > Thank you.
> > Best regards.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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[gmx-users] gmx genion -neutral adds some opposite charge under some conditions

2018-07-04 Thread Vytautas Rakeviius

Hi,

My system has non-zero total charge: 34.09. I do gmx genion -neutral on it, 
I get 35 CL ions dumped into it.
So I continue to get warning "System has non-zero total charge: -0.91".
Fell free to try with your own system.
I think this should be fixed.

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Re: [gmx-users] S-nitrosoylated proteins

2018-06-21 Thread Vytautas Rakeviius

I suggest to check this one:
Han S. Force field parameters for S-nitrosocysteine and molecular dynamics
simulations of S-nitrosated thioredoxin. Biochem Biophys Res Commun. 2008 Dec
12;377(2):612-616. doi: 10.1016/j.bbrc.2008.10.017. Epub 2008 Oct 16. PubMed
PMID: 18929538.
 

On Wednesday, June 20, 2018, 9:57:55 AM GMT+3, Amir Zeb 
 wrote:  
 
 Hello folks,

Which force field has parameters for S-nitrosoylated cysteine?
How may I get it?

Thanks!

Amir
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Re: [gmx-users] Deuterium atoms

2018-06-21 Thread Vytautas Rakeviius

Just change all D to H in structure file IMHO.
 

On Wednesday, June 20, 2018, 5:39:18 PM GMT+3, Hermann, Johannes 
 wrote:  
 
 Dear all,

is there any force field in gromacs (or elsewhere) which can handle 
deuterium atoms?

All the best

Johannes

-- 
__
*Technische Universität München*
*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverfahrenstechnik
Boltzmannstr. 15
D-85748 Garching
Tel: +49 8928915730
Fax: +49 8928915714

Email: j.herm...@lrz.tum.de
http://www.biovt.mw.tum.de/

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Re: [gmx-users] (no subject)

2018-06-21 Thread Vytautas Rakeviius

 
Also depends on what you try to do. Maybe Dry Martini? Look into:ARNAREZ, 
Clément, et al. Dry Martini, a coarse-grained force field for lipid membrane 
simulations with implicit solvent. Journal of chemical theory and computation, 
2014, 11.1: 260-275.
On Thursday, June 21, 2018, 5:22:15 AM GMT+3, Chhaya Singh 
 wrote:  
 
 I want to perform MD simulation using groamcs in implicit solvent. Can you
help me which force field is compatible with which solvent I can take?
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Re: [gmx-users] md simulation of oil hydrocarbon

2018-06-04 Thread Vytautas Rakeviius

 I think you should check as others did ex.: Optimization of the OPLS-AA Force 
Field for Long Hydrocarbons J. Chem. Theory Comput., 2012, 8 (4), pp 1459–1470
 
On Monday, May 28, 2018, 8:23:50 PM GMT+3, Atila Petrosian 
 wrote:  
 
 Hi all,

I want to do md simulation of oil hydrocarbon?

Is there appropriate force field for these hydrocarbons in gromacs?

What I see in gromacs force fields only was related to aminoacids and
nucleotides.

What is your suggestion for md simulation of oil hydrocarbon?

Best,
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Re: [gmx-users] installing Gromacs on windows using cygwin

2018-04-23 Thread Vytautas Rakeviius

If you use bash just add source /usr/local/gromacs/bin/GMXRC to ~/.bashrc file 
as separate line, like:
echo "source /usr/local/gromacs/bin/GMXRC" >> ~/.bashrc
or just use your favorite text editor.
 

On Monday, April 23, 2018, 1:57:02 PM GMT+3, Hossein Geraili 
 wrote:  
 
 Hi,

could you please help me with the search!!!

source /usr/local/gromacs/bin/GMXRC

You may wish to arrange for your login scripts to do this automatically;
please search the web for instructions on how to do this for your shell.

How can I do that command automatically??

Best



‌
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Sender
notified by
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On Sat, Apr 21, 2018 at 4:52 PM, Mark Abraham 
wrote:

> Hi,
>
> Follow
> http://manual.gromacs.org/documentation/current/install-
> guide/index.html#getting-access-to-gromacs-after-installation
> which instructs you to do the same thing you must have done last time. That
> has to be done from each shell, or set up to be true for all shells.
>
> Mark
>
> On Sat, Apr 21, 2018, 13:28 Hossein Geraili  wrote:
>
> > Hi all,
> > I am using Linux, and I followed the installation guide in the Gromacs
> page
> > exactly, and it seems everything was successful for installation of
> Gromacs
> > 2018.1. I also at the end typed "gmx pdb2gmx" and it seems that gromacs
> was
> > installed in all the computer while using that terminal, but when I close
> > the terminal and open a new one with typing the same command it gives the
> > following error:
> > The program 'gmx' is currently not installed. You can install it by
> typing:
> > sudo apt install gromacs
> > what is the problem??
> >
> >
> >
> >
> >
> >
> > ‌
> > [image: Mailtrack]
> > <
> > https://mailtrack.io?utm_source=gmail_medium=signature_campaign=
> signaturevirality4&
> > >
> > Sender
> > notified by
> > Mailtrack
> > <
> > https://mailtrack.io?utm_source=gmail_medium=signature_campaign=
> signaturevirality4&
> > >
> >
> > On Thu, Apr 19, 2018 at 9:42 PM, Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > Surely cygwin has its own cmake package, which you should use rather
> than
> > > compile it yourself.
> > >
> > > Mark
> > >
> > > On Thu, Apr 19, 2018, 18:02 Hossein Geraili 
> > wrote:
> > >
> > > > Hi all,
> > > > I want to install Gromacs on windows 10, and I get the error while
> > > > installing Cmake with cygwin. I tried two different version and the
> > error
> > > > is the same.
> > > >
> > > > gmake: *** No rule to make target '/cygdrive/h/Ph.D/Gromacs/
> > > > Software/cmake-3.10.3/Source/cmAddCustomCommandCommand.cxx', needed
> by
> > > > 'cmAddCustomCommandCommand.o'.  Stop.
> > > > -
> > > > Error when bootstrapping CMake:
> > > > Problem while running gmake
> > > >
> > > > any comment would be appreciated.
> > > > Best
> > > >
> > > >
> > > > --
> > > > Hosein Geraili Daronkola
> > > > M.Sc.Graduated of physical chemistry
> > > > Physical Chemistry,
> > > > Department of Chemistry,
> > > > The Sharif University of Technology.
> > > > geraili_hos...@alum.sharif.edu
> > > > ‌
> > > > [image: Mailtrack]
> > > > <
> > > >
> > https://mailtrack.io?utm_source=gmail_medium=signature_campaign=
> > > signaturevirality4&
> > > > >
> > > > Sender
> > > > notified by
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> > > > --
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> >
> >
> >
> >
> > --
> > Hosein Geraili Daronkola
> > M.Sc.Graduated of physical chemistry
> > Physical Chemistry,
> > Department of Chemistry,
> > The Sharif University of Technology.
> > geraili_hos...@alum.sharif.edu
> > --
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> > * For

Re: [gmx-users] (no subject)

2018-01-02 Thread Vytautas Rakeviius

You should give more details how you try to make residue 44 immobile. Keep in 
mind that some ways to do that can be "defeated" with strong enough pulling. 
Most likely you just have to try few times with different pulling and 
restraining options.
 

On Tuesday, January 2, 2018, 12:30:59 PM GMT+2, Rakesh Mishra 
 wrote:  
 
 Dear sir

I am just a beginner in gromacs. I have installed gromacs 5.1 version.  I
am doing
 pulling for si-rna  (double stranded, 22 nucleotides each ). I am applying
pulling code of  umbrella sampling. Using that, we have chosen 22nd number
residue of chain A is under pulling with constant velocity rate in +ve x
direction.  and residue 44 of  apposite chain B at the apposite end is
taking as reference . Now I am thinking to make the reference residue 44 as
immobile. But when
after simulation I am trying to see the trajectory . Then I Am finding that
the residue n 44 (reference residue of pulling) is also moving and which is
in apposite direction.
even it is showing that reference residue 44 is crossing the box wall in
-ve x direction.

My aim is to pull residue n 22 of chain-A of si-rna by making reference
residue n 44 of chain-B of si-rnA as a immobile, i mean no need for big
motion in apposite direction.

-- 
* Rakesh Kumar Mishra*
*  (RA)CSD  SINP Kolkata, India*

*E-mail - rakesh.mis...@saha.ac.in  *

*Phone n. +91 9473662491, +91877749632*
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Re: [gmx-users] DSSP

2017-12-04 Thread Vytautas Rakeviius


ftp://ftp.cmbi.ru.nl/pub/software/dssp/
There you can find windows .exe version of it.
 

On Tuesday, December 5, 2017, 7:38:44 AM GMT+2, Vidya R 
 wrote:  
 
 Hi gromacs users,

I use gromacs 5.1.4 in *cygwin* (OS windows 7, 64 bit.)

I want to download and install dssp tool.

How to proceed?


Thanks,
Vidya.R
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Re: [gmx-users] water molecule cannot be settled during minimization!!!!

2017-11-07 Thread Vytautas Rakeviius

Investigate same water molecule mentioned in error in vmd or such program 
likely it is in close contact to other molecule.You can move it manually by 
altering coordinates in gro text file into more realistic starting position.Or 
probably even better if you redo your solvatation again (with different 
parameters?).
 

On Monday, November 6, 2017, 7:18:18 AM GMT+2, Seera Suryanarayana 
 wrote:  
 
 Dear gromacs users

I am trying to simulate one protein with 180 residues. During energy
minimization I got the falling error.

Fatal error:

step 26: Water molecule starting at atom 28787 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

I have reduced the em step size from 0.01 to 0.02  as I got this suggestion
from archives. I  still have the same problem. I request you to give a
suggestion how to resolve it.

Thanks in advance
Surya
Graduate student
India.
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Re: [gmx-users] pdb (CTAB) into .GRO

2017-11-03 Thread Vytautas Rakeviius

It seems that ctab.pdb contains residue 'XXX'. Verify that with pdb viewer such 
as pymol etc.
 Residue 'XXX' is not standard amino acid with 3 letter code so in lead to such 
error.Maybe you can delete it with same pdb viewer, or fix that naming error 
somehow. Its up to you to decide.

On Friday, November 3, 2017, 10:49:27 AM GMT+2, Adriano Santana Sanchez 
 wrote:  
 
  Dear all,

 I am a beginner with gromacs and I have already done some online tutorials.
 I am now trying to create from a PDB coordinate file (a CTAB molecule) the
 corresponding .GRO and .TOP files to run MD simulations.

 gmx pdb2gmx -f ctab.pdb -o ctab_processed.gro -water spce

 then choose FF gromos96 53a6 but get error message:

 Residue 'XXX' not found in topology database

I am sure this FF has been used for this molecule before and I cannot

find this CTAB on the residue database. What can I do?

Thanks,
Adriano

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Re: [gmx-users] force field for selinomethionine?

2017-11-02 Thread Vytautas Rakeviius

As far as I see others just replace selenium with sulphur, convert of 
selenomethionine to methionine 
like:https://bmccancer.biomedcentral.com/articles/10.1186/1471-2407-14-775



 

On Wednesday, November 1, 2017, 8:24:10 AM GMT+2, Seera Suryanarayana 
 wrote:  
 
 Dear gromacs users,

I have to do simulations for a peptide which has the selinomethionine. But
regular force fields from gromacs has no information for this residue.
kindly give me information if is there any force field for
selinometheoinine.

Thanks in advance
Surya
Graduate student
India.
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Re: [gmx-users] itp file for aminoacids

Generally you do not need such thing as parameters for amino acids come from 
force filed itself together with Gromacs.It you still want to make one just 
check scientific papers how force fields were created.
 

On Monday, October 30, 2017, 4:41:50 PM GMT+2, rose rahmani 
 wrote:  
 
 hello

how can i make an .itp file for amino acids?
which amino acids is identified in AMBER forcefield?
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Re: [gmx-users] where can i find .itp file for amino acids?

Maybe just rename your custom thr.itp THR and in other places to something else 
to avoid conflict with default version?amber03.ff is in 
gromacs-version/share/top folder. There you can find aminoacids files with 
default amber03 THR.
 

On Saturday, October 28, 2017, 3:54:41 PM GMT+3, rose rahmani 
 wrote:  
 
 Hello,

this is topol.top

---

; Include forcefield parameters
#include "amber03.ff/forcefield.itp"

[ moleculetype ]
; Name            nrexcl
 ZnS                  3

#include "ZnS.itp"
#include "thr.itp"
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif


; Include water topology
#include "./amber03.ff/tip3p.itp"



[ system ]
; Name
LYSOZYME in water

[ molecules ]
; Compound        #mols
 ZnS                1
 THR                1
 SOL              561
-
i get this error
Fatal error:
Atomtype P5 not found
For more information and tips for troubleshooting, please check the GROMACS
-
 thr.itp file

[ moleculetype ]
; molname      nrexcl
THR                1

[ atoms ]
;id type resnr residu atom cgnr  charge    mass
1  P5    1    THR    BB    1      0    72
2  Nda    1    THR    SC1    2      0    0
3  D      1    THR    SC2    3  +0.31    36
4  D      1    THR    SC3    4  -0.31    36

[virtual_sites2]
; Site from      funct a
  2    3    4  1    0.5

[bonds]
;  i    j  funct  length  force.c.
  1    2    1      0.26    9000

[constraints]
;  i    j  funct  length
  3    4    1      0.28

i think the problem is thr.itp file and its not usable for amber03

so what should i do?do you think the problem is that?
i really appreciate you if you help me

with regards
rose
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Re: [gmx-users] Number of coordinates in .gro file does not match topology

You do something wrong. How you solvate?Try something like this:
gmx solvate -cp my_system.gro -cs spc216.gro -o my_system_solv.gro -p topol.top 

On Monday, October 30, 2017, 10:41:31 AM GMT+2, Aishwarya Smriti 
 wrote:  
 
 Hi!

I'm trying to solvate a system of a CNT and a protein molecule. My updated
topology file shows 106275 new solvent molecules added but the .gro file
has only coordinates for 6197 new molecules. I'm using SPC model for
solvating, Please help.

Regards,
Aishwarya Smriti
Senior Undergraduate
Chemical Engineering
Indian Institute of Technology, Delhi
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Re: [gmx-users] Gromacs error

You really need cuda? IF no you can try:cmake .. -DGMX_GPU=OFF
 

On Sunday, October 29, 2017, 7:26:04 AM GMT+2, Kunal Dutta 
 wrote:  
 
 Hi,
I have the following problems

kunal@kunal-HP-Pavilion-Notebook:~/Downloads/gromacs-5.0/build$ cmake ..
-DGMX_BUILD_OWN_FFTW=ON

CMake Warning at src/contrib/fftw/CMakeLists.txt:79 (message):

  The GROMACS build will download FFTW 3.3.3 as requested, but it will not

  know the file it receives is correct.  If you now use



  make



  GROMACS will build and link to FFTW anyway, but there is a possible
security risk if you execute a GROMACS tool that calls this library.
Instead, you can use



  make fftwBuild



  to do just the download and build of FFTW, and then run



  md5sum src/contrib/fftw/fftwBuild-prefix/src/fftw-3.3.3.tar.gz



  to see if it matches 0a05ca9c7b3bfddc8278e7c40791a1c2.  If so, everything

  is OK and you should use



  make



  to proceed with the rest of the GROMACS build. Alternatively, you could
stop using GMX_BUILD_OWN_FFTW, and instead follow the GROMACS installation
instructions to build FFTW yourself.





-- The GROMACS-managed build of FFTW 3 will configure with the following
optimizations: --enable-sse2

-- Configuring done

-- Generating done

-- Build files have been written to: /home/kunal/Downloads/gromacs-5.0/build

kunal@kunal-HP-Pavilion-Notebook:~/Downloads/gromacs-5.0/build$ make

[  1%] Built target fftwBuild

[  1%] Building NVCC (Device) object
src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o

/usr/include/string.h: In function ‘void* __mempcpy_inline(void*, const
void*, size_t)’:

/usr/include/string.h:652:42: error: ‘memcpy’ was not declared in this scope

  return (char *) memcpy (__dest, __src, __n) + __n;

                                          ^

CMake Error at cuda_tools_generated_cudautils.cu.o.cmake:264 (message):

  Error generating file


/home/kunal/Downloads/gromacs-5.0/build/src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o





src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/build.make:383:
recipe for target
'src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_cudautils.cu.o'
failed

make[2]: ***
[src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_cudautils.cu.o]
Error 1

CMakeFiles/Makefile2:1609: recipe for target
'src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all' failed

make[1]: *** [src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all]
Error 2

Makefile:147: recipe for target 'all' failed

make: *** [all] Error 2
-- 
-
Regards.
Kunal Dutta
Senior Research Scholar
Microbiology and Immunology Laboratory
Department of Human Physiology with Community Health
Vidyasagar University, Medinipur-721102
West Bengal, India.
Cell: 9126181933

ORCID ID: -0002-0818-8787
RG: https://www.researchgate.net/profile/Kunal_Dutta2
GS: https://scholar.google.co.in/citations?user=ULby284J=en

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Re: [gmx-users] Potassium channel EM Segmentation fault

2017-10-12 Thread Vytautas Rakeviius

I suggest ignoring/deleting TL and then replacing waters with K randomly 
with:gmx genion.Ofc. it depends what you try to do.
 

On Wednesday, October 11, 2017, 5:01:52 PM GMT+3, Du, Yu  
wrote:  
 
 Dear GMX Users, 


Keyword: metal, energy minimization, segmentation fault 


I have pinpointed the source of EM error. EM succeeds only without potassiums. 


I used PDB 1r3j and changed the TL to K.
You can download the my 1r3j here and reproduce the error like this.


$gmx pdb2gmx -f 1r3j_kchannel.pdb -o 1r3j.gro -ignh -water tip3p
$gmx grompp -f minim.mdp -c 1r3j.gro -p topol.top -o em.tpr
$mpirun -np 20 gmx_mpi mdrun -ntomp 1 -s em.tpr


Thanks for any solutions.


##The minim.mdp file##
define=-DPOSRES
; Parameters describing what to do, when to stop and what to save
integrator  = steep    ; Algorithm (steep = steepest descent minimization)
emtol      = 1000.0    ; Stop minimization when the maximum force < 1000.0 
kJ/mol/nm
emstep      = 0.01      ; 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
cutoff-scheme = verlet
ns_type    = grid      ; Method to determine neighbor list (simple, grid)
rlist      = 1.2      ; Cut-off for making neighbor list (short range forces)
coulombtype = PME      ; Treatment of long range electrostatic interactions
rcoulomb    = 1.2      ; Short-range electrostatic cut-off
rvdw        = 1.2      ; Short-range Van der Waals cut-off
pbc        = xyz      ; Periodic Boundary Conditions
###END##


EM Error

Steepest Descents:
  Tolerance (Fmax)  =  1.0e+03
  Number of steps    =        5
[gpu-new:22930] *** Process received signal ***
[gpu-new:22930] Signal: Segmentation fault (11)
[gpu-new:22930] Signal code: Address not mapped (1)
[gpu-new:22930] Failing at address: 0xfffe01bf6dd0
[gpu-new:22930] [ 0] /lib64/libpthread.so.0[0x383660f710]
[gpu-new:22930] [ 1] 
/home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(+0xe6c36f)[0x2b1966ebe36f]
[gpu-new:22930] [ 2] 
/home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(+0xe6d65f)[0x2b1966ebf65f]
[gpu-new:22930] [ 3] 
/home/duyu/software/gcc-4.9.4/lib64/libgomp.so.1(GOMP_parallel+0x3f)[0x2b196d7a58cf]
[gpu-new:22930] [ 4] 
/home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(_Z17nbnxn_put_on_gridP12nbnxn_searchiPA3_fiPfS3_iifPKiS2_iPiiP16nbnxn_atomdata_t+0xecd)[0x2b1966ec28fd]
[gpu-new:22930] [ 5] 
/home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(dd_partition_system+0x2c67)[0x2b19661ed6b7]
[gpu-new:22930] [ 6] 
/home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(+0xe0379d)[0x2b1966e5579d]
[gpu-new:22930] [ 7] 
/home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(_ZN3gmx8do_steepEP8_IO_FILEP9t_commreciPK8t_filenmPK16gmx_output_env_tiiP11gmx_vsite_tP10gmx_constriP10t_inputrecP10gmx_mtop_tP8t_fcdataP7t_stateP9t_mdatomsP6t_nrnbP13gmx_wallcycleP9gmx_edsamP10t_forcereciiiP12gmx_membed_tffimP23gmx_walltime_accounting+0x353)[0x2b1966e69aa3]
[gpu-new:22930] [ 8] 
gmx_mpi(_ZN3gmx8mdrunnerEP12gmx_hw_opt_tP8_IO_FILEP9t_commreciPK8t_filenmPK16gmx_output_env_tiiPiiiffPKcfSE_SE_SE_SE_iliifffim+0x190a)[0x4101ca]
[gpu-new:22930] [ 9] gmx_mpi(_Z9gmx_mdruniPPc+0x1766)[0x421516]
[gpu-new:22930] [10] 
/home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x2a3)[0x2b19661a5693]
[gpu-new:22930] [11] gmx_mpi(main+0x7c)[0x40cd3c]
[gpu-new:22930] [12] /lib64/libc.so.6(__libc_start_main+0xfd)[0x383621ed1d]
[gpu-new:22930] [13] gmx_mpi[0x40cb79]
[gpu-new:22930] *** End of error message ***
--
mpirun noticed that process rank 0 with PID 0 on node gpu-new exited on signal 
11 (Segmentation fault).
--
###END##


--
Du, Yu
PhD Student,
Shanghai Institute of Organic Chemistry
345 Ling Ling Rd., Shanghai, China. 
Zip: 200032, Tel: (86) 021 5492 5275
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Re: [gmx-users] problem of GB simulation

2017-10-05 Thread Vytautas Rakeviius

Most likely you do something wrong in energy minimization step:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/05_EM.htmlMake
 sure you produce plot similar like in that page with your system before 
proceeding further with minimized system.



 

On Wednesday, October 4, 2017, 9:18:48 PM GMT+3, Albert 
 wrote:  
 
 Hello,

I am using the following .mdp file for protein BG solvent simulations. 
However, the job always failed with the following messages:

vol -0.00! imb F 22% step 144100, remaining wall clock time: 207 s
vol -0.00! imb F 23% step 144200, remaining wall clock time:  207 s
vol -0.00! imb F 23% step 144300, remaining wall clock time:  207 s
vol -0.00! imb F 23% step 144400, remaining wall clock time:  207 s

---
Program gmx mdrun, VERSION 5.1.4
Source code file: 
/icm/home/albert/tmp/gromacs-5.1.4/src/gromacs/mdlib/nsgrid.c, line: 633

Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ind has value 131. It should have been within [ 0 .. 131 ]


The initial system seems to be all right since it is a liner peptide. 
The initial energy of the peptide is also very low. I am not so sure 
whether my .mdp is correct or not


Thank you very much.


define                = -DREST_ON -DSTEP_NVT
integrator              = md
dt                      = 0.001
nsteps                  = 30
nstlog                  = 1000

implicit_solvent    = GBSA
gb_algorithm        = OBC
;nstgbradii          = 1.0
rgbradii        = 1.0
gb_epsilon_solvent    = 80
gb_dielectric_offset    = 0.009
sa_algorithm                = ace-approximation
sa_surface_tension      = 0.0054
pbc            = no
coulombtype            = cut-off

cutoff-scheme          = group
nstlist                = 20
rlist                  = 1.0


tcoupl                  = Nose-Hoover
tc_grps                = Protein
tau_t                  = 1.0
ref_t                  = 310
;
constraints            = h-bonds
constraint_algorithm    = LINCS
;
nstcomm                = 100
comm_mode              = angular
comm_grps              = Protein
;
gen-vel                = yes
gen-temp                = 310
gen-seed                = -1
;
refcoord_scaling        = com

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Re: [gmx-users] purpose of step pdb files during MD

2017-09-07 Thread Vytautas Rakeviius

Energy minimization output explains them. I do not think they are important if 
you get good energy minimization after all.
 

On Thursday, September 7, 2017, 3:41:59 AM GMT+3, Vedat Durmaz 
 wrote:  
 
 
hi guys,

from time to time i'm faced with GMX output files during MD called, e.g. in the 
current case:

step8164372b_n254.pdb
step8164372b_n2.pdb
step8164372c_n254.pdb
step8164372c_n2.pdb

what i know is that they are related to kind of exploding systems. however, i'm 
not really able to interpret their content. if i visualize them in VMD, i see a 
subset of my system surounded by explicit water molecules where the two *n254* 
files contain a larger part of my fibrils (polypeptides) than the *n2* files 
which only show few atoms of one particular amino acid. but if i pick certain 
atoms of the amino acids, they are often not correctly assigned to residue 
names and the atom index shown in VMD is different from the index listed in the 
underlying gro file.

where can i find detailed information about how to interpret the names and 
contents of these files? why are exactly these atoms written to the pdb files 
and what does the file name tell me?

any hint is appreciated.

many thanks,

vedat durmaz


-- 
Vedat Durmaz
Computational Molecular Design
Zuse Institute Berlin (ZIB)
Takustrasse 7
14195 Berlin, Germany
T: +49-30-84185-139
F: +49-30-84185-107
http://www.zib.de/durmaz

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Re: [gmx-users] Error while running perl distances.pl

2017-09-06 Thread Vytautas Rakeviius

Well to better understand what is going on I suggest:* use strict; line tells 
to search for possible problems even if script can go on like it is.Maybe just 
remove it?
 * remove &>/dev/null or even better use other file instead of /dev/null like 
dump.txt
You will see it that system call is all OK from print to screen or to that file.
* Edit all open functions into open or die style. Example:open(OUT, 
">>summary_distances.dat") or die "can not open summary_distances.dat";If that 
file open call fails you will see error like you wrote.* Examine all files 
mentioned in script, they might be bad or not exist, that may hint to possible 
issues.
On Wednesday, September 6, 2017, 10:42:30 AM GMT+3, 가디 장데부 고라크스나트 
<f07...@kist.re.kr> wrote:  
 
 
Hello Vytautas,

I changed the script file to

gmx_mpi_d distance -s md_pull.tpr -f conf${i}.gro -n index.ndx -oall 
dist${i}.xvg -select \'com of group \"lig\" plus com of group \"protein\"\'

 

rest is same

but it showed the same error as previous one.
Error readline() on closed filehandle IN at distances.pl line 16 Use of 
uminitialized value $distance in concatanation (.) or string at distances.pl 
line 30.
 

Could you help me out to solve this issue.

Dr. Changdev G. Gadhe

Post-Doc Researcher,

Convergence Research Center for Diagnosis, Treatment and Care System of 
Dementia,

Korea Institute of Science and Technology, 

Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Korea 

Ph.: +82-10-2779-1546 , Lab: +82-02-958-6850

Email: f07...@kist.re.kr

 

 

 

 

-------Original message---
From: "Vytautas Rakeviius "<vytautas1...@yahoo.com>
To: gmx-us...@gromacs.org,gromacs.org_gmx-users@maillist.sys.kth.se,가디 장데부 
고라크스나트<f07...@kist.re.kr>
Cc.: gadhe.chang...@gmail.com
Sent date: 2017-09-04 15:36:29 GMT +0900 (Asia/Seoul)
Title: Re: [gmx-users] Error while running perl distances.pl
 

 
Script assumes that variable $distance is the second row separated by space in 
the file dist{number}.xvg which appears after execution of system callgmx 
distance -s md_pull.tpr -f conf${i}.gro -n index.ndx -oall dist${i}.xvg -select 
\'com of group \"lig\" plus com of group \"protein\"\'I just think that 
dist{number}.xvg creation fails for you in first place because "gmx distance" 
in the script is not adjusted according to your system.You use _mpi_d in your 
post.   On Monday, September 4, 2017, 5:48:43 AM GMT+3, 가디 장데부 고라크스나트 
<f07...@kist.re.kr> wrote:   Hello Gmx user,  I would like to transport solute 
molecule from the ion channel (intracellular to extracellular site) using 
steered MD and umbrella sampling method to calculate the energy. I followed Dr. 
Lemkul's tutorial and it works fine upto equilibration step but in distance.pl 
it shows some errors. I used the distance of pulling along the Z-axis but still 
it do not work. I found when I use distance as a pull-geometry, solute moves 
away from the channel rather transporting through channel. Then I tried 
direction as a pull-geoetry, then solute transported from the chanel,and 
generated pullf.xvg but not pullx.xvg file. I separated the trajectory using 
trjconv command gmx_mpi_d -f recenter_traj.xtc -s md_pull.tpr -n pro-lig.ndx -o 
conf.gro -sep It generated conformations.Now I would like to calculate the 
COM distance between ion channel (protein) and solute (lig) using perl 
distance.pl but I received following error. Error readline() on closed 
filehandle IN at distances.pl line 16 Use of uminitialized value $distance in 
concatanation (.) or string at distances.pl line 30.Here is the distance.pl 
file which I used for this purpose which was downloaded from Dr. Lemkul's 
tutorial file. -#!/usr/bin/perl -w use strict; # loop g_dist 
command - measure distance in each frame, write to a filefor (my $i=0; $i<=800; 
$i++) {    print "Processing configuration $i...\n";    system("gmx distance -s 
md_pull.tpr -f conf${i}.gro -n index.ndx -oall dist${i}.xvg -select \'com of 
group \"lig\" plus com of group \"protein\"\' &>/dev/null");} # write output to 
single fileopen(OUT, ">>summary_distances.dat"); for (my $j=0; $j<=800; $j++) { 
   open(IN, "<dist${j}.xvg");    my @array = ;     my $distance;     
foreach $_ (@array) {        if ($_ =~ /[#@]/) {            # do nothing, it's 
a comment or formatting line        } else {            my @line = split(" ", 
$_);            $distance = $line[1];        }    }     close(IN);    print OUT 
"$j\t$distance\n";} close(OUT); # clean upprint "Cleaning up...\n"; for (my 
$k=0; $k<=800; $k++) {    unlink "dist${k}.xvg";} exit; 
- this generated the summary_distances.dat with only 
frame numbers but there is no distance column in the file. Please help me t

Re: [gmx-users] Error while running perl distances.pl

2017-09-04 Thread Vytautas Rakeviius

Script assumes that variable $distance is the second row separated by space in 
the file dist{number}.xvg which appears after execution of system call 
gmx distance -s md_pull.tpr -f conf${i}.gro -n index.ndx -oall dist${i}.xvg 
-select \'com of group \"lig\" plus com of group \"protein\"\'I just think that 
dist{number}.xvg creation fails for you in first place because "gmx distance" 
in the script is not adjusted according to your system.You use _mpi_d in your 
post.

 

On Monday, September 4, 2017, 5:48:43 AM GMT+3, 가디 장데부 고라크스나트 
 wrote:  
 
 
Hello Gmx user,


I would like to transport solute molecule from the ion channel (intracellular 
to extracellular site) using steered MD and umbrella sampling method to 
calculate the energy.

I followed Dr. Lemkul's tutorial and it works fine upto equilibration step but 
in distance.pl it shows some errors.

I used the distance of pulling along the Z-axis but still it do not work. I 
found when I use distance as a pull-geometry, solute moves away from the 
channel rather transporting through channel. Then I tried direction as a 
pull-geoetry, then solute transported from the chanel,and generated pullf.xvg 
but not pullx.xvg file.

I separated the trajectory using trjconv command

gmx_mpi_d -f recenter_traj.xtc -s md_pull.tpr -n pro-lig.ndx -o conf.gro -sep

It generated conformations.




Now I would like to calculate the COM distance between ion channel (protein) 
and solute (lig) using perl distance.pl but I received following error.

Error

readline() on closed filehandle IN at distances.pl line 16

Use of uminitialized value $distance in concatanation (.) or string at 
distances.pl line 30.




Here is the distance.pl file which I used for this purpose which was downloaded 
from Dr. Lemkul's tutorial file.

-
#!/usr/bin/perl -w

use strict;

# loop g_dist command - measure distance in each frame, write to a file
for (my $i=0; $i<=800; $i++) {
    print "Processing configuration $i...\n";
    system("gmx distance -s md_pull.tpr -f conf${i}.gro -n index.ndx -oall 
dist${i}.xvg -select \'com of group \"lig\" plus com of group \"protein\"\' 
&>/dev/null");
}

# write output to single file
open(OUT, ">>summary_distances.dat");

for (my $j=0; $j<=800; $j++) {
    open(IN, "

Re: [gmx-users] g_mmpbsa compilation error

2017-09-01 Thread Vytautas Rakeviius

Likely you cmake is far newer than Gromacs (cmake --version to figure that 
out). You should try Gromacs 2016.3
 

On Friday, September 1, 2017, 12:55:14 PM GMT+3, neha chaudhary 
 wrote:  
 
 Hi,

I am trying to compile g_mmpbsa with APBS for gromacs-5.1.2. APBS and
gromacs installed properly but during cmake for g_mmpbsa I am facing the
following error:

-- Found z library: /usr/lib/x86_64-linux-gnu/libz.so
CMake Error at cmake/FindGROMACS.cmake:203 (list):
  list index: 2 out of range (-2, 1)
Call Stack (most recent call first):
  src/CMakeLists.txt:62 (find_package)


-- Found Gromacs include directory: /usr/local/gromacs/include
-- Configuring incomplete, errors occurred!

Can anyone help me with this?


Best Regards,

Neha
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Re: [gmx-users] Gromacs simulation of two or more peptide chain

2017-08-31 Thread Vytautas Rakeviius

Generally that means you starting system is seriously wrong.
Investigate atom 218 and surrounding area. Another atom really close or sth 
like that.


On Thursday, August 24, 2017, 9:36:37 PM GMT+3, Kalyanashis Jana 
 wrote:

Dear all,
I would like to run an MD simulation for two or more peptide chain. I got
the following error in the steepest descent energy minimization step. Could
you please suggest me, how can I do the MD simulation?

Steepest Descents:
  Tolerance (Fmax)  =  1.0e+02
  Number of steps    =      20

WARNING: Listed nonbonded interaction between particles 215 and 219
at distance 3f which is larger than the table limit 3f nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.


Segmentation fault (core dumped)ot=        -nan Fmax= 8.56592e+05, atom=
218


Thanks with regards
Kalyanashis Jana
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Re: [gmx-users] Trouble with gmx distance

2017-08-28 Thread Vytautas Rakeviius

Two atoms for distance calculation have to be in same selection thus program 
expects even number of positions and do not get in my opinion.You could show 
your index.ndx for better investigation.



On Monday, August 21, 2017, 9:24:35 PM GMT+3, Sotirios Dionysios I. Papadatos 
 wrote:

Hi, I am trying to calculate the distance between two atoms, which are defined 
in an index file. The command that I use is:

"gmx distance -f output.gro -s prod.tpr -n index.ndx -oav distance.xvg"

I get the obvious:

"Selection 'atom_name' does not evaluate into an even number of positions (there

are 1 positions)"
The same happens if I use in -f prod.trr
What might be wrong? Any insights on what to look for? What usually gives this 
kind of error?
Feel free to ask for any further information.
Thanks in advance
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Re: [gmx-users] gromacs error

2017-08-28 Thread Vytautas Rakeviius


Make sure you have libfftw3f installed properly. In such case command:whereis 
libfftw3fshould give you location of that file which gmx is unable to find.
On Saturday, August 26, 2017, 1:13:38 PM GMT+3, Neha Gupta 
 wrote:

Hi gromacs users,

How to fix this error?

gmx: error while loading shared libraries: libfftw3f.so.3: cannot open
shared object file: No such file or directory

PATH=$PATH:"/usr/local/gromacs/bin/"

LD_LIBRARY_PATH=$LD_LIBRARY_PATH:"/usr/local/gromacs/share/gromacs/top"



Thanks,
Neha
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Re: [gmx-users] Unable to install 5.1.14

2017-08-28 Thread Vytautas Rakeviius

You have updated boost so you have to update GROMACS too. 2016.3 is the latest
version you should download it.
Another possibility is to downgrade boost to older, but you can bump into other
mish-mash issues. I do not recommend that.

On Sunday, August 27, 2017, 11:36:21 PM GMT+3, Rajat Desikan
wrote:

Dear All,
I had removed gromacs 5.1.14. from my system (Ubuntu 16.04) a while ago,
and I'm having trouble reinstalling it. Cmake runs fine, but the system
repeatedly fails in the make step with this weird error:

[ 3%] Building CXX object src/gromacs/CMakeFiles/
libgromacs.dir/listed-forces/pairs.cpp.o
[ 3%] Building CXX object src/gromacs/CMakeFiles/
libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o
In file included from /usr/local/include/boost/exception/detail/exception_
ptr.hpp:20:0,
from /usr/local/include/boost/exception_ptr.hpp:9,
from /home/entropy/Downloads/gromacs-5.1.4/src/gromacs/
utility/exceptions.h:53,
from /home/entropy/Downloads/gromacs-5.1.4/src/gromacs/
commandline/cmdlineprogramcontext.cpp:62:
/usr/local/include/boost/exception/info.hpp: In member function ‘virtual
boost::shared_ptr
boost::exception_detail::error_info_container_impl::get(const
boost::exception_detail::type_info_&) const’:
/usr/local/include/boost/exception/info.hpp:102:28: error: use of deleted
function
‘boost::shared_ptr::shared_ptr(const
boost::shared_ptr&)’
return p;
^
In file included from /usr/local/include/boost/shared_ptr.hpp:17:0,
from /home/entropy/Downloads/gromacs-5.1.4/src/gromacs/
commandline/cmdlineprogramcontext.h:54,
from /home/entropy/Downloads/gromacs-5.1.4/src/gromacs/
commandline/cmdlineprogramcontext.cpp:47:
/usr/local/include/boost/smart_ptr/shared_ptr.hpp:168:25: note:
‘boost::shared_ptr::shared_ptr(const
boost::shared_ptr&)’ is
implicitly declared as deleted because ‘boost::shared_ptr’ declares a move constructor or move
assignment operator

There are similar errors after this, and make fails. I have updated boost
on my system (version 58), and my system has the latest upgrades. Can
anyone please point out the way ahead? I've exhausted all easy options (Eg.
cleanly remove all gromacs associated files, redownload, untar and try to
install).

My cmake command is:
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
-DCMAKE_INSTALL_PREFIX=/usr/local/gromacs514 -DGMX_USE_RDTSCP=off

I've tried other permutations of the above command (without
-DGMX_USE_RDTSCP=off
for instance) and nothing seems to work.

Thank you for your time.

Regards,
Rajat

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Prof. Narendra M Dixit's Lab (no 1),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
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Re: [gmx-users] GROMACS with Torque: Job stuck

2017-08-25 Thread Vytautas Rakeviius

Check log files in server_logs and mom_logs folders in the TORQUE_HOME. You can 
find there what is going on in more detail.



On Friday, August 25, 2017, 4:25:03 PM GMT+3, Souparno Adhikary 
 wrote:

Hi,

This is related to running GROMACS through mpirun and Torque. After I
installed Torque in our lab cluster, I went on to test GROMACS using a
simple run. I wrote a Torque script as follows:

#!/bin/sh
#PBS -N asyn
#PBS -q batch
#PBS -l nodes=4:ppn=4
#PBS -l walltime=120:00:00
cd $PBS_O_WORKDIR
cat $PBS_NODEFILE>nodes
mpirun -np 16 gmx_mpi mdrun -deffnm asyn_10ns

After I submit this file using qsub command, the job is properly
showing using pbsnodes command in other mom units.

But, the job stays as R in 00:00:00 in the list. I presume, this might
be an error from my part in setting up GROMACS with Torque. I compiled
GROMACS with -DGMX_MPI=ON

The nodes file is not written and the job stays stuck.

Can anyone familiar with job scheduling help me in this regard???


Souparno Adhikary,
CHPC Lab,
Department of Microbiology,
University of Calcutta.
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Re: [gmx-users] gmx distance

2017-08-25 Thread Vytautas Rakeviius

Enter both groups into one line.



On Friday, August 25, 2017, 2:43:47 PM GMT+3, Sergio Manzetti 
 wrote:

Hello, I am trying to find the average distance between two groups in a 
trajectory, defined by the index.ndx file and the traj.xtc, 

the options are 


Available static index groups: 
Group 0 "System" (1 atoms) 
Group 1 "DNA" (1333 atoms) 
Group 2 "NA" (71 atoms) 
Group 3 "CL" (31 atoms) 
Group 4 "DEHP" (66 atoms) 
Group 5 "Ion" (102 atoms) 
Group 6 "NA" (71 atoms) 
Group 7 "CL" (31 atoms) 
Group 8 "DEHP" (66 atoms) 
Group 9 "Other" (66 atoms) 
Group 10 "NA" (71 atoms) 
Group 11 "CL" (31 atoms) 
Group 12 "DEHP" (66 atoms) 
Group 13 "Water" (31830 atoms) 
Group 14 "SOL" (31830 atoms) 
Group 15 "non-Water" (1501 atoms) 
Group 16 "Water_and_ions" (31932 atoms) 
Group 17 "DEHP" (66 atoms) 
Group 18 "DNA" (1333 atoms) 
Specify any number of selections for option 'select' 
(Position pairs to calculate distances for): 
(one per line,  for status/groups, 'help' for help, Ctrl-D to end) 
> 1 
Selection '1' parsed 
> 4 
Selection '4' parsed 
> 


however, then, which command to issue to start the distance generation? 

Thanks 

Sergio Manzetti 

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Re: [gmx-users] installation_server machine_error

2017-08-23 Thread Vytautas Rakeviius

Well it seams that you compiled Gromacs with mpi support so now you should run 
it with sth. like that: mpirun -np 1 /opt/apps/gromacs/4.6.6/bin/gmx 
pdb2gmx_mpi -f 1aki.pdb -o 1AKI_processed.gro -water spceRun:man mpirunfor more 
details.
On Wednesday, August 23, 2017, 10:42:47 AM GMT+3, Kashif 
 wrote:

dear sir
after installing gromacs on server, I could not able to run the simulation.
It always shows "-bash: command not found".
 when I tried to locate the pdb2gmx, it showed the path as-
/opt/apps/gromacs/4.6.6/bin/pdb2gmx_mpi

When I run the following command by using the path as below--- I
got error

[kashif@Server protein]$ /opt/apps/gromacs/4.6.6/bin/gmx pdb2gmx -f
1aki.pdb -o 1AKI_processed.gro -water spce

-bash: /opt/apps/gromacs/4.6.6/bin/gmx: No such file or directory

[kashif@Server protein]$ /opt/apps/gromacs/4.6.6/bin/pdb2gmx -f 1aki.pdb -o
1AKI_processed.gro -water spce

-bash: /opt/apps/gromacs/4.6.6/bin/pdb2gmx: No such file or directory


Although after looking into the installed gromacs bin directory
(/opt/apps/gromacs/4.6.6/bin), I found all the packages of gromacs...

[root@Server bin]# ls
completion.bash  g_dos_mpi          GMXRC.bash      g_sigeps_mpi
completion.csh    g_dyecoupl_mpi    GMXRC.csh        g_sorient_mpi
completion.zsh    g_dyndom_mpi      GMXRC.zsh        g_spatial_mpi
demux.pl          genbox_mpi        g_nmeig_mpi      g_spol_mpi
do_dssp_mpi      genconf_mpi        g_nmens_mpi      g_tcaf_mpi
editconf_mpi      g_enemat_mpi      g_nmtraj_mpi    g_traj_mpi
eneconv_mpi      g_energy_mpi      g_options_mpi    g_tune_pme_mpi
g_anadock_mpi    genion_mpi        g_order_mpi      g_vanhove_mpi
g_anaeig_mpi      genrestr_mpi      g_pme_error_mpi  g_velacc_mpi
g_analyze_mpi    g_filter_mpi      g_polystat_mpi  g_wham_mpi
g_angle_mpi      g_gyrate_mpi      g_potential_mpi  g_wheel_mpi
g_bar_mpi        g_h2order_mpi      g_principal_mpi  g_x2top_mpi
g_bond_mpi        g_hbond_mpi        g_protonate_mpi  make_edi_mpi
g_bundle_mpi      g_helix_mpi        g_rama_mpi      make_ndx_mpi
g_chi_mpi        g_helixorient_mpi  g_rdf_mpi        md.log
g_cluster_mpi    g_hydorder_mpi    g_rmsdist_mpi    mdrun_mpi
g_clustsize_mpi  g_kinetics_mpi    g_rmsf_mpi      mk_angndx_mpi
g_confrms_mpi    g_lie_mpi          g_rms_mpi        pdb2gmx_mpi
g_covar_mpi      g_luck_mpi        grompp_mpi      tpbconv_mpi
g_current_mpi    g_mdmat_mpi        g_rotacf_mpi    trjcat_mpi
g_density_mpi    g_membed_mpi      g_rotmat_mpi    trjconv_mpi
g_densmap_mpi    g_mindist_mpi      g_saltbr_mpi    trjorder_mpi
g_densorder_mpi  g_morph_mpi        g_sans_mpi      xplor2gmx.pl
g_dielectric_mpi  g_msd_mpi          g_sas_mpi        xpm2ps_mpi
g_dipoles_mpi    gmxcheck_mpi      g_select_mpi
g_disre_mpi      gmxdump_mpi        g_sgangle_mpi
g_dist_mpi        GMXRC              g_sham_mpi


Kindly suggest me the proper commands so that I can run the simulation.


regards
kashif
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Re: [gmx-users] use INTERFACE Force Field

2017-06-28 Thread Vytautas Rakeviius

Hello,
Possible bot not easy.Look into Gromacs folder share/top/ all force fields sit 
there as text files your will have to make ITERFACE text files in same format 
and layout.What you download as ITERFACE force field are also text files with 
parameters, but layout is for different programs.
 

On Wednesday, June 28, 2017 4:05 PM, Мижээ Батсайхан 
 wrote:
 

 Dear gmx users,

I would like to use gromacs 5.1v with INTERFACE force field. Please, any
advice and suggestions, thank you.

Best regards,
Miji
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Re: [gmx-users] Simulations stop running after reaching specific time step

2017-06-27 Thread Vytautas Rakeviius

Maybe post your mdp file. There are settings about writing out and default 
values if you add nothing too.
 

On Tuesday, June 27, 2017 10:44 AM, Shobha Sharma 
 wrote:
 

 Hello,

I am submitting few simulations, after providing the wall time enough to
finish the jobs. But after reaching a certain time step, in case of all
jobs, the output files are not written beyond that time step.

For example if I check my .log file, using 'tail -f md.log'  I find that it
is not writing anything even though job is running. It utilizes whole wall
time given and ends without writing any further time steps.
In the end it does not even write about any problem faced. Job ends due to
end of wall time.

What might be the reason behind this?

-- 
Thanks and Regards,
Shobha
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[gmx-users] Adding multiple different ligands with acpype

2017-06-20 Thread Vytautas Rakeviius

Hello,
I try to add multiple and different ligands with acpype and bump into issue 
"Invalid order for directive atomtypes" discussed before 
(https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2008-July/035223.html)I
 can comment out other ligands leaving one and then it seems OK.
I do as said in that discussion:I add:
#include "ligand1.acpype/ligand1_GMX.itp"
#include "ligand2.acpype/ligand2_GMX.itp"into topol.top right after:; Include 
forcefield parameters
#include "amber99sb-ildn.ff/forcefield.itp"
And in bottom ([ molecules ]) I add:ligand1    1
ligand2    1
Exact error:Fatal error:
Syntax error - File isofluraneS_GMX.itp, line 3
Last line read:
'[ atomtypes ]'
Invalid order for directive atomtypes
How I can fix this?
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Re: [gmx-users] error in running md

2017-06-13 Thread Vytautas Rakeviius

Check structure, mainly atom numbers given in messages. Bad contacts or 
something.
 

On Tuesday, June 13, 2017 1:45 PM, VARSHA RANI  
wrote:
 

 Hi,

I ran minim.mdp for my system with 3456 atoms.  But lowest energy after
minimization is positive.

*here is th screen output*

Step= 4509, Dmax= 4.5e-05 nm, Epot=  4.06554e+02 Fmax= 9.86206e+00, atom=
3521

writing lowest energy coordinates.

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

Steepest Descents converged to Fmax < 10 in 4510 steps
Potential Energy  =  4.0655389e+02
Maximum force    =  9.8620596e+00 on atom 352
Norm of force    =  3.3500545e+00

NOTE: 16 % of the run time was spent in pair search,
      you might want to increase nstlist (this has no effect on accuracy)


*Below is txt of minim.mdp file *

; minim.mdp - used as input into grompp to generate em.tpr
integrator    = steep        ; Algorithm (steep = steepest descent
minimization)
emstep          = 0.01        ; Energy step size
;emtol        = 1000.0      ; Stop minimization when the maximum force <
1000.0 kJ/mol/nm
nsteps        = 50    ; Maximum number of (minimization) steps to
perform
; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist            = 10              ; Frequency to update the neighbor
list and long range forces
rlist            = 2        ; cut-off for making neighbour list (short
range forces)
cutoff-scheme      = Verlet
ns_type            = grid        ; Method to determine neighbor list
(simple, grid)
coulombtype        = PME        ; Treatment of long range electrostatic
interactions
rcoulomb        = 0.9        ; Short-range electrostatic cut-off
rvdw            = 0.9        ; Short-range Van der Waals cut-off
pbc            = xyz        ; Periodic Boundary Conditions (yes/no)



regards
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Re: [gmx-users] gromacs-5.1.4 installation issue

2017-05-24 Thread Vytautas Rakeviius

This kind of issues can mean that you moved compiled binary to quite different 
machine.
Though I am not sure what you did.
Compile on the same machine you are going to use or at least as similar as 
possible (same Linux ver. with same updates). 

On Wednesday, May 24, 2017 3:13 PM, abhisek Mondal  
wrote:
 

 Hi,

  I have been trying to install latest version of gromacs (Gromacs-5.1.4)
in my cluster.

Installation went without any error. But whenever I'm giving the command:
gmx_mpi
An error report comes:
gmx_mpi: /lib64/libz.so.1: no version information available (required by
/app/gromacs-5.1.4/lib64/libgromacs_mpi.so.1)
gmx_mpi: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found
(required by /app/gromacs-5.1.4/lib64/libgromacs_mpi.so.1)


Can you please help me out here, regarding what is going wrong here.

Thank you.

-- 
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*
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Re: [gmx-users] Problems install GROMACS 2016.3 on Ubuntu 17.04

2017-05-24 Thread Vytautas Rakeviius


Hmm It might be problem that you removed compilers. Wonder what you have now.If 
you still have problem please post output of:
g++ -v && gcc -v
Command. 

On Wednesday, May 24, 2017 3:14 PM, Mark Abraham <mark.j.abra...@gmail.com> 
wrote:
 

 Hi,

Using a gcc version also entails linking to the standard library that comes
along with it, ie libstdc++.so. By default, it will link at run time to the
version that shipped with the package. For any sufficiently new compiler,
that won't work (by design) because the library and the compiler evolve
together. To tell the resulting gromacs which new standard library to link
to, you need to set the LD_LIBRARY_PATH environment variable, e.g. for bash
on a 64-bit Linux system (almost all of them these days):

export LD_LIBRARY_PATH=/path/to/your/gcc/lib64:$LD_LIBRARY_PATH

in the shell from which you want to run gmx.

We should probably look into having cmake hack on the RPATH so this can
work more automagically.

Mark

On Wed, May 24, 2017 at 12:12 PM Steffen Graether <graet...@uoguelph.ca>
wrote:

> Hi Vytautas,
>
> I should have mentioned that I had deleted the ‘build’ directory and tried
> the cmake command again, but I received the same error.
>
> I had installed a large number of different compilers (clang-3.8,
> clang-4.0, gcc-5) to get my CUDA installation to work but thought I had
> removed them all afterwards (just ran apt-get remove again to delete
> clang-4.0). Still getting the same error.
>
> Regards,
> Steffen
>
> Date: Wed, 24 May 2017 08:45:57 + (UTC)
>
> > From: Vytautas Rakeviius <vytautas1...@yahoo.com>
> > To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org>,
> >      "gromacs.org_gmx-users@maillist.sys.kth.se"
> >      <gromacs.org_gmx-users@maillist.sys.kth.se>
> > Subject: Re: [gmx-users] Problems install GROMACS 2016.3 on Ubuntu
> >      17.04
> > Message-ID: <743319698.939458.1495615557...@mail.yahoo.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > Ubuntu 17.04 should give you quite up-to date gcc and co.
> > Make sure you try this on clean folder: remove everything download and
> try again. Maybe some old files interfering.
> >
> >
> >    On Wednesday, May 24, 2017 4:14 AM, Steffen Graether <
> graet...@uoguelph.ca> wrote:
> >
> >
> > Hi,
> >
> > I?ve tried installing GROMACS 2016.3 on Ubuntu 17.04. I?ve checked that
> gcc-6 and g++6 are installed, but when running cmake? I get the following
> error:
> >
> > -- Performing Test CXX11_STDLIB_PRESENT - Failed
> > CMake Error at cmake/gmxTestCXX11.cmake:139 (message):
> > ? This version of GROMACS requires C++11-compatible standard library.?
> Please
> > ? use a newer compiler, or a newer standard library, or use the GROMACS
> 5.1.x
> > ? release.? See the installation guide for details.
> > Call Stack (most recent call first):
> > ? CMakeLists.txt:164 (gmx_test_cxx11)
> >
> > Searching for this problem I find a few references to having an up to
> date gcc, but nothing else. Can anyone point me in the right direction to
> fix this?
> >
> > Thanks,
> > Steffen
> >
> >
> >
> >
> > --
> > 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
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
> >
> >
> >
> > --
> >
> > Message: 4
> > Date: Wed, 24 May 2017 11:28:55 +0200
> > From: "Kamps, M." <m.ka...@student.rug.nl>
> > To: gromacs.org_gmx-users@maillist.sys.kth.se
> > Subject: [gmx-users] Problem with accelerations
> > Message-ID:
> >      <
> cacskku3niwewt7d8o-nteqmgq+vwpg0mfmbud_s-0kcpaov...@mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > Mark,
> >
> > I'm not really sure what you mean by technique. I assume NEMD stands
> > for Non-equilibrium MD? That is the case in my simulation..
> >
> > About my simulation: I am trying to simulate a fluid flow between
> > surfaces. Two atomistic surfaces of gold atoms have been created at
> > Z=0 and Z=z, where z is the top of the box. These surfaces are fixed.
> > In between is a fluid that should be accelerated in order to create a
> > flow. This is done by applying a constant acceleration in the X
> > direction via the com

Re: [gmx-users] Problems install GROMACS 2016.3 on Ubuntu 17.04

2017-05-24 Thread Vytautas Rakeviius

Ubuntu 17.04 should give you quite up-to date gcc and co.
Make sure you try this on clean folder: remove everything download and try 
again. Maybe some old files interfering.
 

On Wednesday, May 24, 2017 4:14 AM, Steffen Graether  
wrote:
 

 Hi,

I’ve tried installing GROMACS 2016.3 on Ubuntu 17.04. I’ve checked that gcc-6 
and g++6 are installed, but when running cmake  I get the following error:

-- Performing Test CXX11_STDLIB_PRESENT - Failed
CMake Error at cmake/gmxTestCXX11.cmake:139 (message):
  This version of GROMACS requires C++11-compatible standard library.  Please
  use a newer compiler, or a newer standard library, or use the GROMACS 5.1.x
  release.  See the installation guide for details.
Call Stack (most recent call first):
  CMakeLists.txt:164 (gmx_test_cxx11)

Searching for this problem I find a few references to having an up to date gcc, 
but nothing else. Can anyone point me in the right direction to fix this?

Thanks,
Steffen




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Re: [gmx-users] User Defined Potentials

2017-04-25 Thread Vytautas Rakeviius

Inside GROMACS folder go share/top/ you will find folders for force fileds like 
gromos53a5.ff/ there are files with water topology like tip3p.itp you can write 
your own using them as examples.
 

On Tuesday, April 25, 2017 12:58 AM, Ommair Ishaque  wrote:
 

 Hi,

I am Phd physics phd student at University of Delaware. I am using GROMACS
for calculation of solvation energy of argon or methane in water. But Our
water model has additional interaction terms other than already define in
GROMACS. *Can we add our own interaction terms in GROMACS? If yes how?*

And one of my senior colleagues was telling me in past, GROMACS had no
quaternion algorithm for rigid molecules. It handles rigid molecules using
SHAKE/RATTLE/LINCS. If this is still the case, I am not entirely sure how
we will be able to use it for our water model (CC-5spol) which has at least
25 sites. *If there is now a means of truly propagating the motion of rigid
molecules without SHAKE/RATTLE/LINCS, this will be great.*

I am looking forward for your positive reply. Thanks

Ommair Ishaque
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Re: [gmx-users] make

2017-04-20 Thread Vytautas Rakeviius

Its stated in:"GNU version! gcc versions later than 5 are not supported!"The 
most simple solution is just download newer GROMACS version like 2016.3.
 

On Thursday, April 20, 2017 1:53 PM, Anshul Lahariya 
 wrote:
 

 hello,

 i am a new user installing gromacs on my machine.
  during the installation, i found an error in make command. kindly
suggest we correct it.


error:-
[root@dhcppc99 gromacs-5.1.4-build]# make
[  1%] Built target fftwBuild
[  1%] Building NVCC (Device) object
src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/libgromacs_generated_copyrite_gpu.cu.o
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are
deprecated, and may be removed in a future release (Use
-Wno-deprecated-gpu-targets to suppress warning).
In file included from /usr/local/cuda/include/cuda_runtime.h:78:0,
                from :0:
/usr/local/cuda/include/host_config.h:119:2: error: #error -- unsupported
GNU version! gcc versions later than 5 are not supported!
 #error -- unsupported GNU version! gcc versions later than 5 are not
supported!
  ^
CMake Error at libgromacs_generated_copyrite_gpu.cu.o.Release.cmake:207
(message):
  Error generating

/home/gromacs-5.1.4-build/src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/./libgromacs_generated_copyrite_gpu.cu.o


src/gromacs/CMakeFiles/libgromacs.dir/build.make:63: recipe for target
'src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/libgromacs_generated_copyrite_gpu.cu.o'
failed
make[2]: ***
[src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/libgromacs_generated_copyrite_gpu.cu.o]
Error 1
CMakeFiles/Makefile2:2319: recipe for target
'src/gromacs/CMakeFiles/libgromacs.dir/all' failed
make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
Makefile:160: recipe for target 'all' failed
make: *** [all] Error 2
[root@dhcppc99 gromacs-5.1.4-build]#
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Re: [gmx-users] Gromacs - MD run

2017-04-20 Thread Vytautas Rakeviius

Selected force field determines what will be pushed and what will be pulled 
during MD run. Which one you use? Maybe just try other.
 

On Thursday, April 20, 2017 1:20 PM, Mariusz Wierzbowski 
 wrote:
 

 Dear Gromacs users,

I am not sure what is the problem with my init file, I have a pdb file 
1rep.pdb i performed mdrun for it for 150 ns. After each run(I divied the run 
to 5 ns steps, it gave me 25 runs)I perfomed all of the runs. Than I wanted 
to check if the pdb files were ok. I checeked the pdb file gained from gro 
file with ediconf and the pdb looked good, the model looked stable for 16 
steps. Then I checked the nr 17 step and the model has ds DNA splitted into 2 
ss DNA one is close to the protein and second is below the protein. This 
situation is for rest of the steps from 17-25. What could go wrong? What is 
the possible explanation of this? Any suggestions ?

Thanks for all the help

Mariusz

P.S

Earlier I got a suggestion that I should perform -pbc nojump but that does 
not affect the gro file so the pdb still looks bad.
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Re: [gmx-users] Gcc

2017-04-20 Thread Vytautas Rakeviius

Its quite problematic to alter existing Linux install in such way and better 
download proper gromacs version or such.Another possibility just select 
appropriate Linux distribution and version ex. my Slackware 14.2 comes with gcc 
5.3.0.
 

On Thursday, April 20, 2017 1:42 PM, Anshul Lahariya 
 wrote:
 

 hello,

I want to change my gcc and want to install gcc version later than 5.
what can i do so i can change the version of gcc to gcc-4.9.4
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Re: [gmx-users] PROTEIN FOLDING

2017-04-06 Thread Vytautas Rakeviius

Yes, you can open all structural output files with VMD. Or Chimera (tools MD so 
on).
 

On Thursday, April 6, 2017 9:56 AM, Neha Gupta  
wrote:
 

 Hi gromacs users,


I have run 2ns simulation of protein ligand complex using NVT ensemble
(after equilibration).


I want to know whether there is a structural/conformational change in the
protein especially in the active site where, the ligand forms hydrogen
bonds with the protein during simulation.


Can we visualize it? Is it possible?

Please let me know.


Thanks,
Neha
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[gmx-users] Building box arround given membrane with gmx solvate. As small as possible.

2017-04-06 Thread Vytautas Rakeviius

Hello,
I want to build box around my membrane with gmx solvate or sth. Ofc. I do not 
want water in side gap between membrane and box.
I do like this:
gmx editconf -f gap_processed.gro -o gap_newbox.gro -c -bt cubicI expect -d 0 
so everything packed in box as tightly as possible, but still after "gmx 
solvate" I see some water between box and membrane side.Maybe this is normal? 
Maybe I should do small run to let water flow away? Or maybe my command is 
wrong and I should make tight box in other way?
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Re: [gmx-users] how to know solvent molecule number

Oh sorry number of atoms you will have to divide by number of atoms in 
ethanolamine. 

On Wednesday, April 5, 2017 4:45 PM, Vytautas Rakeviius 
<vytautas1...@yahoo.com> wrote:
 

 head -n 2 obj.gro | tail -n 1Print number of molecules in obj.gro file. 
Solvate then do same on new file:
head -n 2 obj_solv.gro | tail -n 1All you need is difference.
 

On Wednesday, April 5, 2017 4:13 PM, Chintan Bhagat <cbb.chin...@gmail.com> 
wrote:
 

 Hello,

I want to do stimulation of my protein in solvent, ethanolamine (different
percentage).
I have made box of 1 nm and then using command
"gmx solvate -cp 1AKI_newbox.gro -cs ethanolamine.gro -o 1AKI_solv.gro -p
topol.top",
As per my knowledge, i solvated my protein in ethanolamine.
Now I want to know the number of ethanolamine molecule present in box. Then
I looked in to *.top* file but no information is availble in the file (SOL).
(As per intruction, program is only hard-coded to update the topology in
the case of water).
I found increase in number of molecules from 7200 to 128004 in
/home/lab1/Desktop/md2/1AKI_processed.gro.gro and 1AKI_solv.gro,
respectively. It means something is inserted in box (must be
ethanolamine!-my guess)
How can i know number of ethanolamine molecules?


for reference please find attched files.

Thanking you in advance.
-- 
Regards,
Chintan Bhagat
Research scholar,
Veer Narmad South Gujarat University,
India
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Re: [gmx-users] how to know solvent molecule number

head -n 2 obj.gro | tail -n 1Print number of molecules in obj.gro file. Solvate 
then do same on new file:
head -n 2 obj_solv.gro | tail -n 1All you need is difference.
 

On Wednesday, April 5, 2017 4:13 PM, Chintan Bhagat  
wrote:
 

 Hello,

I want to do stimulation of my protein in solvent, ethanolamine (different
percentage).
I have made box of 1 nm and then using command
"gmx solvate -cp 1AKI_newbox.gro -cs ethanolamine.gro -o 1AKI_solv.gro -p
topol.top",
As per my knowledge, i solvated my protein in ethanolamine.
Now I want to know the number of ethanolamine molecule present in box. Then
I looked in to *.top* file but no information is availble in the file (SOL).
(As per intruction, program is only hard-coded to update the topology in
the case of water).
I found increase in number of molecules from 7200 to 128004 in
/home/lab1/Desktop/md2/1AKI_processed.gro.gro and 1AKI_solv.gro,
respectively. It means something is inserted in box (must be
ethanolamine!-my guess)
How can i know number of ethanolamine molecules?


for reference please find attched files.

Thanking you in advance.
-- 
Regards,
Chintan Bhagat
Research scholar,
Veer Narmad South Gujarat University,
India
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Re: [gmx-users] gmx mdrun

"my CPU switches off automatically"? Can you expain what actually happens. 
Windows go to sleep etc?Also you should do such things on Linux, cygwin is not 
that fast as you see in warning message.
 

On Sunday, April 2, 2017 11:24 AM, Neha Gupta  
wrote:
 

 Hi gromacs users,


I am using Gromacs 5.1.1 in windows cygwin.

When I run long calculations my CPU switches off automatically (just before
writing the coordinate file .gro) . How to prevent this and ensure
longevity of CPU?

Running on 1 node with total 8 logical cores
Hardware detected:
  CPU info:
    Vendor: AuthenticAMD
    Brand:  AMD FX-8370E Eight-Core Processor
    Family: 21  model:  2  stepping:  0



I also observed these in log file


SIMD instructions most likely to fit this hardware: AVX_128_FMA
 SIMD instructions selected at GROMACS compile time: SSE4.1


Binary not matching hardware - you might be losing performance.
SIMD instructions most likely to fit this hardware: AVX_128_FMA
SIMD instructions selected at GROMACS compile time: SSE4.1


The current CPU can measure timings more accurately than the code in gmx
was configured to use. This might affect your simulation speed as accurate
timings are needed for load-balancing.
Please consider rebuilding gmx with the GMX_USE_RDTSCP=ON CMake option.



Thanks,
Neha
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Re: [gmx-users] (no subject)

You can use acpype to prepare ligands for MD run.
 

On Wednesday, April 5, 2017 1:01 PM, maria khan 
 wrote:
 

 Dear Erik..

I have studied the manuals of gromacs and from that i came to know that
gromacs use united atom ff thats why i asked and in manuals many things has
been explained by quantum basis,,which is not understandable for me.

How can i find ff parameters for my ligand of interest?? also if
ff parameters are not in published form then it means i will not be able to
use that ligand for MD run?? My ligand of interest is alkaloid. and i dont
know how can i make the parameters for it.

Thank you.
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Re: [gmx-users] CHARMM27 hates my DMPC

2017-04-04 Thread Vytautas Rakeviius

Thanks, I reused DMPC layers from CHARMM-GUI after some editing.I was able to 
pin-down issue here, test 
file:http://www.mediafire.com/file/usuv55c3j505ec2/test.pdbI can do:gmx pdb2gmx 
-f test.pdb -o test.gro -water spce
Without error. But if I do:gmx pdb2gmx -f test.pdb -o test.gro -water spce 
-ignhI get error about hydrogen which I try to ignore. Very strange for me. 
-ignh option is not possible with CHARMM ff?

On Tuesday, April 4, 2017 3:59 PM, Justin Lemkul <jalem...@vt.edu> wrote:

On 4/4/17 8:52 AM, Vytautas Rakeviius wrote:
> Hello,
> I have my system with DMPC bilayers in pdb and try to convert it into GROMACS 
> input. Because system is with lipids I think chose CHARMM27 ff. But still I 
> get lots of warnings like that:
>
> https://pastebin.com/K8dHKkUi
> Also I add my DMPC pdb as example. What should I do? Rename all my DMPC 
> atoms?Thanks for all suggestions.
>
>

This is the same with any force field; the atom names have to match the force 
field's expectations.

If you're just trying to build a DMPC bilayer, construct one using CHARMM-GUI. 
It's guaranteed to have CHARMM-compliant nomenclature (and you should be using 
CHARMM36 for lipids, anyway, because the CHARMM27 parameters are not nearly as 
good for lipids).

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==

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[gmx-users] CHARMM27 hates my DMPC

2017-04-04 Thread Vytautas Rakeviius

Hello,
I have my system with DMPC bilayers in pdb and try to convert it into GROMACS 
input. Because system is with lipids I think chose CHARMM27 ff. But still I get 
lots of warnings like that: 

https://pastebin.com/K8dHKkUi
Also I add my DMPC pdb as example. What should I do? Rename all my DMPC 
atoms?Thanks for all suggestions.


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Re: [gmx-users] Energy Miinimization question

2017-04-03 Thread Vytautas Rakeviius

As you set smaller emtol you do better and longer minimization. So with 1000 
you stop simulation way before polymer forms some rings. You can check video 
with VMD Chimera or something.
 

On Saturday, April 1, 2017 8:25 PM, Mishelle Oña  
wrote:
 

 Hello everybody,

I have a question about the final conformation after energy minimization. I am 
simulating a polymer in vacuo and I used steepest descent method for energy 
minimization. When I use an emtol=1000 the structure I get is linear. Then I 
tried an emtol=30 because another study about the same polymer used this value 
but the final structure has some rings, I am not sure why this happened.

Thanks for your help.

Mishelle
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Re: [gmx-users] Regarding structure conformation

2017-04-03 Thread Vytautas Rakeviius

MD can not simulate chemical reactions. What you can do prepare different forms 
with acpype and compare all in some way.
 

On Monday, April 3, 2017 6:51 AM, Dilip H N  
wrote:
 

 Hello,

I have a non zwitterionic glycine molecule, and have solvated it with
water, created topology and ran the simulation...and during EM, NVT, MD
runs the non zwitterionic form of glycine is still as it is, it hasn't got
converted into zwitterionic form (which is the most stable form of glycine
in water/solvent)...
So how can i convert non zwitterionic glycine form to its zwitterionic
form..??
Ideally it should get converted into its most stable form during solvation,
but why is it not getting converted..?? how can i solve this issue..?? Is
there anything wrong.??

Thank you
-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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Re: [gmx-users] FAD parameters in CHRAMm36 ff

2017-03-31 Thread Vytautas Rakeviius

I think you should use cgenff for FAD in such case. They are compatible and can 
by used together.
 

On Friday, March 31, 2017 9:29 AM, Amir Zeb  wrote:
 

 Hello Folks,

I want to simulate a protein where FAD is included as co-factor. I will use
CHARMm36 ff but I don't know the residue ID for FAD in this particular
forcefield. Anyone please let me know by which name FAD is represented in
CHARMm36 ff?

Thanks in advance!

~Amir
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Re: [gmx-users] Pull Code constant value

2017-03-28 Thread Vytautas Rakeviius

I suggest trial and error in quite short runs without wasting time on waiting 
for next day or so. Really large k can create segmentation faults or 
"cannonball into wall" like effects in MD movie.
 

On Tuesday, March 28, 2017 2:43 PM, Souparno Adhikary 
 wrote:
 

 Hi all,

I am trying to pull a DNA molecule out of its binding pocket in a protein.
I took Justin Lemkul's tutorial as the guiding script and started with k1
value of 1000. As it seemed, it needed more force to detach the molecule
from its binding partner. Can you tell me how to estimate/calculate this
value or it simply based on the trial-and-error method?

Also, what problems can take place if the value is large (huge, I guess)?

Thanks,

Souparno Adhikary
University of Calcutta.
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Re: [gmx-users] Regarding structure

2017-03-24 Thread Vytautas Rakeviius

If you interested in just one glycine one possible solution is to prepare it 
with acpype instead. It respects your hydrogens and you can set charge as 
command line option.

On Friday, March 24, 2017 6:14 AM, Jonathan Saboury  
wrote:

 Please be considerate to others and only post a topic once. Not only does
multiple posts annoy others but it greatly diminishes your chances of
receiving help.

I unfortunately do not have the expertize to help you, but I'm sure someone
will soon.

- Jonathan

On Thu, Mar 23, 2017 at 9:08 PM, Dilip H N 
wrote:

> Hello,
> The glycine .pdb that i have is a non zwitter ionic form, and from this if
> i want to create a topology file from the following command as -
> gmx pdb2gmx -f gly.pdb -o gly.gro
> and selected charmm FF i am getting the following msg...
>
> Processing chain 1 'A' (10 atoms, 1 residues)
> Identified residue GLY1 as a starting terminus.
> Identified residue GLY1 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
> Start terminus GLY-1: GLY-NH3+
> End terminus GLY-1: COO-
>
> It is showing tht glycine as zwitterionic form, But i dnt want it to be in
> zwitterionic form... How can i solve this issue..??
>
> --
> With Best Regards,
>
> DILIP.H.N
> Research Scholar,
> Department of Chemistry, NITK.
>
>
>
>   Sent with Mailtrack
>  referral=cy16f01.di...@nitk.edu.in=22>
> --
> Gromacs Users mailing list
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[gmx-users] g_membed or alternative on GROMACS 2016

2017-03-23 Thread Vytautas Rakeviius

Hello, 

I am reading "Computational Electrophysiology: The Molecular Dynamics of Ion 
Channel Permeation and Selectivity in Atomistic Detail" (
http://dx.doi.org/10.1016/j.bpj.2011.06.010) and it mentions tool called:

g_membed
but I can not find it on recent GROMACS 2016 versions. It was removed or 
renamed or what happened?
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Re: [gmx-users] COEFFICIENT FOR LINEAR INTERACTION ENERGY IN PROTEIN LIGAND COMPLEX

2017-03-23 Thread Vytautas Rakeviius

Hello,
Here one recent paper with new parameters for LIE 
derived:https://www.ncbi.nlm.nih.gov/pubmed/26373640You just extract energy 
terms and then do some MLR fitting with R or something. Maybe even recent 
version of MS Excel can do this.


 

On Thursday, March 23, 2017 7:24 AM, Neha Gupta  
wrote:
 

 Hi gromacs users,

How to derive Linear Interaction Energy Coefficients for protein ligand
complex?

Since the parameters vary for different force fields, how to approach this
problem?

Can anyone suggest relevant papers?

Thanks
Neha
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Re: [gmx-users] Error in free energy calculation

As article name in reference says PLUMED can be used for free-energy 
calculations with molecular dynamics. 

On Thursday, March 16, 2017 1:23 PM, Hannes Loeffler 
<hannes.loeff...@stfc.ac.uk> wrote:
 

 On Thu, 16 Mar 2017 10:09:58 +
Vytautas Rakeviius <vytautas1...@yahoo.com> wrote:

> You should try to add PLUMED (plumed.org) to GROMACS for such
> things.Bonomi, M., Branduardi, D., Bussi, G., Camilloni, C., Provasi,
> D., Raiteri, P., ... & Parrinello, M. (2009). PLUMED: A portable
> plugin for free-energy calculations with molecular dynamics. Computer
> Physics Communications, 180(10), 1961-1972. 

I'm not sure how this is helping the original request.  Does Plumed
handle the method being used here?  If not, what would the alternative
be and what would be the advantage of that?


>    On Thursday, March 16, 2017 11:50 AM, Tasneem Kausar
> <tasneemkausa...@gmail.com> wrote: 
> 
>  Dear All
> 
> I am trying to perform free energy calculations of a protein drug
> system. I am using Gromacs-5.1.4 for this purpose. decoulpe molecule
> type i.e. drug molecule is defined in separate drug.itp file. From
> the discussions of mailing list I have found that this is not a
> problem. To obtain the equilibrium values for protein-ligand
> restraint 15 ns simulation was performed. Here is the last section of
> topology file. ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
> #include "drug.itp"
> [ intermolecular_interactions ]
> [ bonds ]
> ;    i    j  type    r0A    r1A    r2A    fcA    r0B    r1B    r2B
> fcB
>   1444  3118    10    0.591  0.591  10.0  0.0    0.591  0.591  10.0
> 4184.000
> 
> [ angle_restraints ]
> ;  ai    aj    ak    al  type    thA      fcA    multA  thB      fcB
> multB
>   1431  1444  3118  1444    1    52.35    0.0    1    52.35
> 41.840    1 1444  3118  3120  3118    1  118.14    0.0    1  118.14
>   41.840    1
> 
> [ dihedral_restraints ]
> ;  ai    aj    ak    al  type    phiA    dphiA  fcA    phiB      dphiB
> fcB
>   1444  1431  1444  3118    1    -99.41  0.0    0.0    -99.41    0.0
> 41.840
>   1431  1444  3118  3120    1    17.49    0.0    0.0    17.49    0.0
> 41.840
>   1444  3118  3120  3119    1    -6.49  0.0    0.0    -6.49    0.0
> 41.840
> ; Include water topology
> #include "gromos54a7.ff/spc.itp"
> 
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct      fcx        fcy        fcz
>   1    1      1000      1000      1000
> #endif
> 
> ; Include topology for ions
> #include "gromos54a7.ff/ions.itp"
> 
> [ system ]
> ; Name
> DUMM in water t= 1.0
> [ molecules ]
> ; Compound        #mols
> Protein_chain_A    1
> DRG                1
> SOL            17685
> 
> Is there any default position for [ intermolecular_interaction ] in
> topology file.
> Since I am using a drug.itp file for drug molecule. Numbering in itp
> file starts from 1. Is atom number in itp file needed to be modified?
> 
> 
> grompp gives many warning  and 1 error
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.9#
> 
> WARNING 1 [file em_steep_0.mdp, line 78]:
>   Unknown left-hand 'pull_geometry' in parameter file
> 
> 
> 
> WARNING 2 [file em_steep_0.mdp, line 78]:
>   Unknown left-hand 'pull_dim' in parameter file
> 
> 
> 
> WARNING 3 [file em_steep_0.mdp, line 78]:
>   Unknown left-hand 'pull_start' in parameter file
> 
> 
> 
> WARNING 4 [file em_steep_0.mdp, line 78]:
>   Unknown left-hand 'pull_init1' in parameter file
> 
> 
> 
> WARNING 5 [file em_steep_0.mdp, line 78]:
>   Unknown left-hand 'pull_ngroups' in parameter file
> 
> 
> 
> WARNING 6 [file em_steep_0.mdp, line 78]:
>   Unknown left-hand 'pull_group0' in parameter file
> 
> 
> 
> WARNING 7 [file em_steep_0.mdp, line 78]:
>   Unknown left-hand 'pull_group1' in parameter file
> 
> 
> 
> WARNING 8 [file em_steep_0.mdp, line 78]:
>   Unknown left-hand 'pull_k1' in parameter file
> 
> 
> 
> WARNING 9 [file em_steep_0.mdp, line 78]:
>   Unknown left-hand 'pull_kB1' in parameter file
> 
> 
> 
> NOTE 1 [file em_steep_0.mdp]:
>   With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20.
> Note that with the Verlet scheme, nstlist has no effect on the
> accuracy of your simulation.
> 
> Setting the LD random seed to 1259182625
> Generated 226 of the 1711 non-bonded parameter combinations
> 
> ---
> Program gmx grompp, VERSION 5.1.4
> Source code file:
> /home/shahid/Software/gromacs-5.1.4/src/gromacs/gmxpreprocess

Re: [gmx-users] LINEAR INTERACTION ENERGY

You need separate energygrps (http://manual.gromacs.org/online/mdp_opt.html 
(output control) for all average components in LIE equation: Protein, Ligand 
and solvent.Probably you will need "gmx energy" too to extract average 
Ligand-solvent interaction terms from edr file before inserting them into "gmx 
lie".And make sure you know LIE equation, check that paper I gave you or 
references about LIE inside it.
 

On Thursday, March 16, 2017 1:26 PM, Kulkarni R <alumniphys...@hotmail.com> 
wrote:
 

 
Thanks.


You have mentioned "proper energy groups" in mdp file


Could you please say more about it?


Thanks,

Kulkarni.R


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Vytautas 
Rakeviius <vytautas1...@yahoo.com>
Sent: Thursday, March 16, 2017 10:29 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] LINEAR INTERACTION ENERGY

Basically you do two MD runs one with ligand in water other with ligand in 
protein. You must set proper energygrps in mdp file so you get 2 edr files from 
runs and in the end you use "gmx lie" 
(http://manual.gromacs.org/programs/gmx-lie.html) to compute difference between 
those two edr files.You might check this paper too:
gmx lie - GROMACS<http://manual.gromacs.org/programs/gmx-lie.html>
manual.gromacs.org
Synopsis gmx lie [-f [.edr>]] [-o [.xvg>]] [-nice ] [-b ] [-e ] [-dt ] [-[no]w] 
[-xvg ] [-Elj ] [-Eqq ] [-Clj ] [-Cqq ] [-ligand ]


Curr Comput Aided Drug Des. 2015;11(3):237-44.

    On Thursday, March 16, 2017 12:15 PM, Kulkarni R 
<alumniphys...@hotmail.com> wrote:


 Hi gromacs users,

In order to calculate delta G (Gibbs free energy) for protein ligand binding, 
what are the steps to be followed in Linear interaction energy?


Are there any tutorials for the same?


Thanks,

Kulkarni.R
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Re: [gmx-users] LINEAR INTERACTION ENERGY

Basically you do two MD runs one with ligand in water other with ligand in 
protein. You must set proper energygrps in mdp file so you get 2 edr files from 
runs and in the end you use "gmx lie" 
(http://manual.gromacs.org/programs/gmx-lie.html) to compute difference between 
those two edr files.You might check this paper too:
Curr Comput Aided Drug Des. 2015;11(3):237-44. 

On Thursday, March 16, 2017 12:15 PM, Kulkarni R 
 wrote:
 

 Hi gromacs users,

In order to calculate delta G (Gibbs free energy) for protein ligand binding, 
what are the steps to be followed in Linear interaction energy?


Are there any tutorials for the same?


Thanks,

Kulkarni.R
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Re: [gmx-users] Error in free energy calculation

You should try to add PLUMED (plumed.org) to GROMACS for such things.Bonomi, 
M., Branduardi, D., Bussi, G., Camilloni, C., Provasi, D., Raiteri, P., ... & 
Parrinello, M. (2009). PLUMED: A portable plugin for free-energy calculations 
with molecular dynamics. Computer Physics Communications, 180(10), 1961-1972. 

On Thursday, March 16, 2017 11:50 AM, Tasneem Kausar 
 wrote:
 

 Dear All

I am trying to perform free energy calculations of a protein drug system.
I am using Gromacs-5.1.4 for this purpose. decoulpe molecule type i.e. drug
molecule is defined in separate drug.itp file. From the discussions of
mailing list I have found that this is not a problem. To obtain the
equilibrium values for protein-ligand restraint 15 ns simulation was
performed. Here is the last section of topology file.
 ; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
#include "drug.itp"
[ intermolecular_interactions ]
[ bonds ]
;    i    j  type    r0A    r1A    r2A    fcA    r0B    r1B    r2B
fcB
  1444  3118    10    0.591  0.591  10.0  0.0    0.591  0.591  10.0
4184.000

[ angle_restraints ]
;  ai    aj    ak    al  type    thA      fcA    multA  thB      fcB
multB
  1431  1444  3118  1444    1    52.35    0.0    1    52.35    41.840    1
  1444  3118  3120  3118    1  118.14    0.0    1  118.14    41.840    1

[ dihedral_restraints ]
;  ai    aj    ak    al  type    phiA    dphiA  fcA    phiB      dphiB
fcB
  1444  1431  1444  3118    1    -99.41  0.0    0.0    -99.41    0.0
41.840
  1431  1444  3118  3120    1    17.49    0.0    0.0    17.49    0.0
41.840
  1444  3118  3120  3119    1    -6.49  0.0    0.0    -6.49    0.0
41.840
; Include water topology
#include "gromos54a7.ff/spc.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct      fcx        fcy        fcz
  1    1      1000      1000      1000
#endif

; Include topology for ions
#include "gromos54a7.ff/ions.itp"

[ system ]
; Name
DUMM in water t= 1.0
[ molecules ]
; Compound        #mols
Protein_chain_A    1
DRG                1
SOL            17685

Is there any default position for [ intermolecular_interaction ] in
topology file.
Since I am using a drug.itp file for drug molecule. Numbering in itp file
starts from 1. Is atom number in itp file needed to be modified?


grompp gives many warning  and 1 error
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.9#

WARNING 1 [file em_steep_0.mdp, line 78]:
  Unknown left-hand 'pull_geometry' in parameter file



WARNING 2 [file em_steep_0.mdp, line 78]:
  Unknown left-hand 'pull_dim' in parameter file



WARNING 3 [file em_steep_0.mdp, line 78]:
  Unknown left-hand 'pull_start' in parameter file



WARNING 4 [file em_steep_0.mdp, line 78]:
  Unknown left-hand 'pull_init1' in parameter file



WARNING 5 [file em_steep_0.mdp, line 78]:
  Unknown left-hand 'pull_ngroups' in parameter file



WARNING 6 [file em_steep_0.mdp, line 78]:
  Unknown left-hand 'pull_group0' in parameter file



WARNING 7 [file em_steep_0.mdp, line 78]:
  Unknown left-hand 'pull_group1' in parameter file



WARNING 8 [file em_steep_0.mdp, line 78]:
  Unknown left-hand 'pull_k1' in parameter file



WARNING 9 [file em_steep_0.mdp, line 78]:
  Unknown left-hand 'pull_kB1' in parameter file



NOTE 1 [file em_steep_0.mdp]:
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
  that with the Verlet scheme, nstlist has no effect on the accuracy of
  your simulation.

Setting the LD random seed to 1259182625
Generated 226 of the 1711 non-bonded parameter combinations

---
Program gmx grompp, VERSION 5.1.4
Source code file:
/home/shahid/Software/gromacs-5.1.4/src/gromacs/gmxpreprocess/topio.c,
line: 755

Fatal error:
Syntax error - File complex.top, line 19956
Last line read:
'[ intermolecular_interactions ]'
Invalid order for directive intermolecular_interactions
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Here are mdp parameters

; Options for the decoupling
sc-alpha                = 0.5
sc-coul                  = no
sc-power                = 1
sc-sigma                = 0.3
couple-moltype          = DRG
couple-lambda0          = none
couple-lambda1          = vdw-q
couple-intramol          = no
nstdhdl                  = 10
; No velocities during EM
gen_vel                  = no
; options for bonds
constraints              = all_bonds
constraint-algorithm    = lincs
continuation            = no
lincs-order              = 12
pull          = no
pull_geometry  = distance
pull_dim      = N N Y
pull_start    = yes
pull_init1    = 0.654
pull_ngroups  = 1
pull_group0    = a_1444
pull_group1    = a_3118
pull_k1        = 0.0  ; kJ*mol^(-1)*nm^(-2)
pull_kB1      = 4184  ; kJ*mol^(-1)*nm^(-2)

since I have defined restraint parameters

Re: [gmx-users] Distance restraints on two TYR OH groups so that they are together