Re: [gmx-users] topology

[Jakub Krajniak]

Did you try mktop ? (http://www.aribeiro.net.br/mktop)


On 02.03.2017 05:23, RAHUL SURESH wrote:

Dear Justin

Is there anything I can do to make this job easier?

On Thu, Mar 2, 2017 at 1:02 AM, Justin Lemkul  wrote:



On 3/1/17 2:19 PM, RAHUL SURESH wrote:


Dear Justin

What is the error here?
I don't understand it.
Can you be little more precise?



The long and short of it TopolGen is very crudely coded and atom order
matters because the script makes a lot of assumptions.  Your input PDB file
has atoms grouped by element (O,O,C,C,C,C,H...) so TopolGen can't figure
out what any of the actual functional groups are, so you get basically
default atom types for everything.

-Justin


On Wed, Mar 1, 2017 at 1:58 AM, Justin Lemkul  wrote:



On 2/28/17 3:24 AM, RAHUL SURESH wrote:

This is my itp file(only a part)

I have highlighted two errors.. there are 19 such errors.
If I can know the reason for the error exactly it would be of a great
help
to me.


TopolGen relies on atom ordering to guess what the proper parameters

should be. It's pretty limited in what it can do.  A coordinate file that
simply groups atoms by element is going to produce a totally garbage
topology, unfortunately.

-Justin


[ atoms ]

;   nr   type  resnr residue  atom   cgnr charge   mass
typeBchargeB  massB
  1   opls_154  1UNK  O  0 -0.580921
15.99940
  2   opls_154  1UNK  O  0 -0.635654
15.99940
  3   opls_516  1UNK  C  1 -0.112257
12.01100
  4   opls_516  1UNK  C  2 -0.163224
12.01100
  5   opls_516  1UNK  C  3  0.228741
12.01100
  6   opls_516  1UNK  C  4 -0.304756
12.01100
  7   opls_516  1UNK  C  5 -0.312217
12.01100
  8   opls_145  1UNK  C  6  0.120569
12.01100
  9   opls_145  1UNK  C  7  0.151897
12.01100
 10   opls_145  1UNK  C  8  0.231044
12.01100
 11   opls_516  1UNK  C  9 -0.401751
12.01100
 12   opls_516  1UNK  C 10 -0.403094
12.01100
 13   opls_145  1UNK  C 11 -0.150352
12.01100
 14   opls_145  1UNK  C 12  0.193129
12.01100
 15   opls_145  1UNK  C 13 -0.161115
12.01100
 16   opls_516  1UNK  C 14 -0.471874
12.01100
 17   opls_145  1UNK  C 15  0.100725
12.01100
 18   opls_145  1UNK  C 16 -0.153943
12.01100
 19   opls_516  1UNK  C 17 -0.330577
12.01100
 20   opls_516  1UNK  C 18 -0.229875
12.01100
 21   opls_135  1UNK  C 19 -0.229884
12.01100
 22   opls_135  1UNK  C 20 -0.237230
12.01100
 23   opls_135  1UNK  C 21 -0.404861
12.01100
 24   opls_140  1UNK  H 21  0.135257
1.00800
 25   opls_140  1UNK  H 21  0.154010
1.00800
 26   opls_140  1UNK 2H 21  0.142643
1.00800
 27   opls_140  1UNK 1H 21  0.133623
1.00800
 28   opls_140  1UNK 2H 21  0.137323
1.00800
 29   opls_140  1UNK 1H 21  0.167475
1.00800
 30   opls_140  1UNK 1H 21  0.135348
1.00800
 31   opls_140  1UNK 2H 21  0.153851
1.00800
 32   opls_140  1UNK 3H 21  0.138487
1.00800
 33   opls_140  1UNK 1H 21  0.137087
1.00800
 34   opls_140  1UNK 2H 21  0.146500
1.00800
 35   opls_140  1UNK 3H 21  0.148972
1.00800
 36   opls_140  1UNK  H 21  0.103605
1.00800
 37   opls_140  1UNK  H 21  0.127061
1.00800
 38   opls_140  1UNK 1H 21  0.143100
1.00800
 39   opls_140  1UNK 2H 21  0.137525
1.00800
 40   opls_140  1UNK 3H 21  0.140672
1.00800
 41   opls_140  1UNK  H 21  0.106416
1.00800
 42   opls_140  1UNK 1H 21  0.134610
1.00800
 43   opls_140  1UNK 2H 21  0.126890
1.00800
 44   opls_140  1UNK 2H 21  0.132690
1.00800
 45   opls_140  1UNK 1H 21  0.124796
1.00800
 46   opls_140  1UNK  H 21  0.371894
1.00800
 47   opls_140  1UNK 1H 21  0.120642
1.00800
 48   opls_140  1UNK 2H 21  0.117792
1.00800
 49   opls_140  1UNK 2H 21  0.125342
1.00800
 50   opls_140  1UNK 1H 21  0.122930
1.00800
 51   opls_140  1UNK 1H 21  0.130012
1.00800
 52   opls_140  1UNK 2H 21  0.129674
1.00800
 53   opls_140  1   

[gmx-users] gmx sans crashes or return nan's

[Jakub Krajniak]

Hi,

I've tried to run gmx sans tool on our trajectory but unfortunately it 
crashes or returns -nan.
The crash is when it is compiled in Release mode. I have used the latest 
2016 release.


GROMACS:  gmx sans, version 2016

gmx_mpi sans -f traj_comp.xtc -s topol.tpr -dt 10 -nt 10
Select a group: 0
Selected 0: 'System'
Reading frame   0 time0.000   Segmentation fault (core dumped)

With CMAKE_BUILD_TYPE=Debug, the run does not cause the segmentation 
fault error but the sq.xvg and pr.xvg contain -nan ; This

is independent of selected groups.

Maybe someone know what could be the reason of such behavior? Here are 
the .tpr and .xtc files:

https://www.dropbox.com/s/29ftayq9uhfipjz/sans_50_50.zip?dl=0

Best regards,

Jakub

--
Jakub Krajniak
KU Leuven, Dept. Computer Science lokaal: 01.41
+32 477 68 84 04 / +32 16 37 39 92

# This file was created Thu Sep 22 09:28:16 2016
# Created by:
#:-) GROMACS - gmx sans, 2016 (-:
# 
# Executable:   
/user/leuven/307/vsc30783/vsc_data/software/2015a/GROMACS/2016/bin/gmx_mpi
# Data prefix:  /user/leuven/307/vsc30783/vsc_data/software/2015a/GROMACS/2016
# Working dir:  /ddn1/vol1/site_scratch/leuven/307/vsc30783/sans_50_50
# Command line:
#   gmx_mpi sans -f traj_comp.xtc -s topol.tpr -dt 10 -nt 10 -sq 
/user/leuven/307/vsc30783/sq.xvg -pr /user/leuven/307/vsc30783/pr.xvg
# gmx sans is part of G R O M A C S:
#
# Green Red Orange Magenta Azure Cyan Skyblue
#
@title "G(r)"
@xaxis  label "Distance (nm)"
@yaxis  label "Probability"
@TYPE xy
  0.10  -nan
  0.30  -nan
  0.50  -nan
  0.70  -nan
  0.90  -nan
  1.10  -nan
  1.30  -nan
  1.50  -nan
  1.70  -nan
  1.90  -nan
  2.10  -nan
  2.30  -nan
  2.50  -nan
  2.70  -nan
  2.90  -nan
  3.10  -nan
  3.30  -nan
  3.50  -nan
  3.70  -nan
  3.90  -nan
  4.10  -nan
  4.30  -nan
  4.50  -nan
  4.70  -nan
  4.90  -nan
  5.10  -nan
  5.30  -nan
  5.50  -nan
  5.70  -nan
  5.90  -nan
  6.10  -nan
  6.30  -nan
  6.50  -nan
  6.70  -nan
  6.90  -nan
  7.10  -nan
  7.30  -nan
  7.50  -nan
  7.70  -nan
  7.90  -nan
  8.10  -nan
  8.30  -nan
  8.50  -nan
  8.70  -nan
  8.90  -nan
  9.10  -nan
  9.30  -nan
  9.50  -nan
  9.70  -nan
  9.90  -nan
 10.10  -nan
 10.30  -nan
 10.50  -nan
 10.70  -nan
 10.90  -nan
 11.10  -nan
 11.30  -nan
 11.50  -nan
 11.70  -nan
 11.90  -nan
 12.10  -nan
 12.30  -nan
 12.50  -nan
 12.70  -nan
 12.90  -nan
 13.10  -nan
 13.30  -nan
 13.50  -nan
 13.70  -nan
 13.90  -nan
 14.10  -nan
 14.30  -nan
 14.50  -nan
 14.70  -nan
 14.90  -nan
 15.10  -nan
 15.30  -nan
 15.50  -nan
 15.70  -nan
 15.90  -nan
 16.10  -nan
 16.30  -nan
 16.50  -nan
 16.70  -nan
 16.90  -nan
 17.10  -nan
 17.30  -nan
 17.50  -nan
 17.70  -nan
 17.90  -nan
 18.10  -nan
 18.30  -nan
 18.50  -nan
 18.70  -nan
 18.90  -nan
 19.10  -nan
 19.30  -nan
 19.50  -nan
 19.70  -nan
 19.90  -nan
# This file was created Thu Sep 22 09:28:16 2016
# Created by:
#:-) GROMACS - gmx sans, 2016 (-:
# 
# Executable:   
/user/leuven/307/vsc30783/vsc_data/software/2015a/GROMACS/2016/bin/gmx_mpi
# Data prefix:  /user/leuven/307/vsc30783/vsc_data/software/2015a/GROMACS/2016
# Working dir:  /ddn1/vol1/site_scratch/leuven/307/vsc30783/sans_50_50
# Command line:
#   gmx_mpi sans -f traj_comp.xtc -s topol.tpr -dt 10 -nt 10 -sq 
/user/leuven/307/vsc30783/sq.xvg -pr /user/leuven/307/vsc30783/pr.xvg
# gmx sans is part of G R O M A C S:
#
# God Rules Over Mankind, Animals, Cosmos and Such
#
@title "I(q)"
@xaxis  label "q (nm^-1)"
@yaxis  label "s(q)/s(0)"
@TYPE xy
  0.00  1.00
  0.01  -nan
  0.02  -nan
  0.03  -nan
  0.04  -nan
  0.05  -nan
  0.06  -nan
  0.07  -nan
  0.08  -nan
  0.09  -nan
  0.10  -nan
  0.11  -nan
  0.12  -nan
  0.13  -nan
  0.14  -nan
  0.15  -nan
  0.16  -nan
  0.17  -nan
  0.18  -nan
  0.19  -nan
  0.20  -nan
  0.21  -nan
  0.22  -nan
  0.23  -nan
  0.24  -nan
  0.25  -nan
  0.26  -nan
  0.27  -nan
  

Re: [gmx-users] read trr file

[Jakub Krajniak]

On 26.11.2014 03:04, 石锐 wrote:

Hi all,

I have generated a large .trr file (~500 G) from a simulation. To save the 
space, I just want to write a C/C++ code to read and manipulate the binary .trr 
file directly rather than convert it to a readable .gro or .pdb file. However, 
I cannot find the format of .trr file from the manual. Is there anyone who 
knows how to read the .trr file ?



You can very easily read the .trr file via the Python MDAnalysis library:
https://code.google.com/p/mdanalysis/

Best regards,
Jakub Krajniak

--
Jakub Krajniak, Computer Science Department @ KU Leuven
tel. +32 16 3 27061 / mob. +32 477 688 404
room: 200a 01.41

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Re: [gmx-users] the growth of the molecule

[Jakub Krajniak]

 before
posting!

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--
Jakub Krajniak, Computer Science Department @ KU Leuven
mob. +32 477 688 404
room: 200a 01.41


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[gmx-users] AdResS - adress_reference_coords

[Jakub Krajniak]

Dear,

I have a question related to the AdResS scheme. Mainly how I should 
interpret the width of ex and hy zone in the case of xsplits.


Is it that adress_reference_coords define the center of the ex zone. So 
on the -x and x I have a ex/2.0 and then I have a region with width hy?


Like on this scheme:
|--| hy | ex/2.0 |rf| ex/2.0 | hy |--|


Or I should interpreted it as:
|--| hy | ex |rf| ex | hy |--|

where rf is a reference coords

The same question is for the sphere scheme.

Best regards,
Jakub Krajniak


--
Jakub Krajniak, Computer Science Department @ KU Leuven
mob. +32 477 688 404
room: 200a 01.41

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[gmx-users] mixing tabulated potential with force field for the AdResS

[Jakub Krajniak]

Dear,

I am trying to run the system that is composite of the atomistic part 
and the coarse grained part. Together it should be coupled by the AdResS.
For the atomistic part I have already run the simulation with the opls 
force field. It run without issue and gave correct density under STP.
The coarse grained part is described by two tables, the bonded 
interaction by table_b1.xvg and the non-bonded interaction by 
table_A_A.xvg. This also run correctly. Under STP I am getting almost 
correct value of density.
Now, when it comes to coupling it together I am following the procedure 
from the 6.11 (user-manual). My index file contains the group for 
coarse-grained and group for all-atom molecules.

When I run the grompp -v -n I am getting warning:

Using sigma/epsilon based combination rules with user supplied 
potential function may produce unwanted results


I could skip it but I don't understand what is the meaning of this warning?

If I skip it then when I run the mdrun_d -v I am getting error with
information about missing table.xvg and tablep.xvg.
I don't understand why I have to provide the table for pair interaction? 
(it wasn't required in the all-atom case - assume that opls/ff handled it).

The same for the table.xvg file, the colombtype is set to cut-off.
I could probably provide empty table.xvg and tablep.xvg but still want 
to understand how it works.


Best regards,
Jakub

--
Jakub Krajniak, Computer Science Department @ KU Leuven
mob. +32 477 688 404
room: 200a 01.41

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[gmx-users] mixing tabulated potential with force field for the AdResS

[Jakub Krajniak]

Dear,

I am trying to run the system that is composite of the atomistic part
and the coarse grained part. Together it should be coupled by the AdResS.
For the atomistic part I have already run the simulation with the opls
force field. It run without issue and gave correct density under STP.
The coarse grained part is described by two tables, the bonded
interaction by table_b1.xvg and the non-bonded interaction by
table_A_A.xvg. This also run correctly. Under STP I am getting almost
correct value of density.
Now, when it comes to coupling it together I am following the procedure
from the 6.11 (user-manual). My index file contains the group for
coarse-grained and group for all-atom molecules.
When I run the grompp -v -n I am getting warning:

Using sigma/epsilon based combination rules with user supplied
potential function may produce unwanted results

I could skip it but I don't understand what is the meaning of this warning?

If I skip it then when I run the mdrun_d -v I am getting error with
information about missing table.xvg and tablep.xvg.
I don't understand why I have to provide the table for pair interaction?
(it wasn't required in the all-atom case - assume that opls/ff handled it).
The same for the table.xvg file, the colombtype is set to cut-off.
I could probably provide empty table.xvg and tablep.xvg but still want
to understand how it works.

Best regards,
Jakub

--
Jakub Krajniak, Computer Science Department @ KU Leuven
mob. +32 477 688 404
room: 200a 01.41

Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
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