[gmx-users] Fwd:

[saranya]

Hi,
I have done protein-drug simulations for 100ns. While calculating the hydrogen
bond between the protein-drug complex I am getting only 2 hydrogen bonds.
The number of H-bond formation is very low I have a question about is there
any influence of the drug in my protein?

With Regards,

*Saranya Vasudevan,*

*Research Scholar,*

*Molecular Quantum Mechanics Laboratory,*

*Department of Physics,*

*Bharathiar University,*

*Coimbatore-46*
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Re: [gmx-users] ligand

[‪farial tavakoli‬ ‪]

Hi Justin 

Thank you so much
with best 
Farial


  From: Justin Lemkul 
 To: gmx-us...@gromacs.org 
 Sent: Monday, 14 August 2017, 16:35:58
 Subject: Re: [gmx-users] ligand
   


On 8/14/17 2:03 AM, ‪farial tavakoli‬ ‪ wrote:
> Dear Justin
> Thanks for your advice.Now I am trying to create a .gro file from the united 
> atom pdb structure file obtained from ATB  by using :editconf -f xxx.pdb -o 
> xxx.gro
> but faced to this warning:
> WARNING: all CONECT records are ignored
> would you please advice me how can i solve this problem?

You don't.  You don't need connectivity information from the PDB because 
it's all in the topology.  This really shouldn't be a "warning," rather 
an informative note.

-Justin

-- 
==

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

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

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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[gmx-users] Scaling in gromacs

[praveen kumar]

Dear GMX users

In order to benchmark my simulation system I would like to know  in gromacs
which code scales linearly till 10K cores?

Thanks
Best Regards
Praveen


-- 
Thanks & Regards
Dr. Praveen Kumar Sappidi,
DST-National Postdoctoral Fellow
Computational Nanoscience Lab
Chemical Engineering Department,
IIT Kanpur
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[gmx-users] Kudos to trjconv -pbc cluster coder

[Dallas Warren]

Whoever it was that did the coding for the cluster option, you did a
great job :-)

Been using it on some rather initially messy looking coordinate and
trajectory files in the last couple of weeks. Transforms them into
things of beauty.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.
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[gmx-users] Question on gmx_wham with two reaction coordinates.

[Yuanchao Liu (MSU)]

Hi all

I have a question on dealing with two reaction coordinates by gmx_wham. I
did umbrella sampling on glucose 6-phosphate molecule on a poly-Lys peptide
surface. Because the peptide is neither cylindrical nor spherical
symmetric, I have to restraint each window around a specific point, using
two reaction coordinates (distance and direction). As results, the ligand's
trajectory looks pretty well. It was restraint around a specific points,
instead of going around a sphere surface when I used 'distance' alone.

However, I got some issue using WHAM for analysis. That is, GROMACS seems
not to allow me to use WHAM with two pull geometry (distance and
direction). So I have to pick only one reaction coordinate to do the
analysis. When I run regular wham, I got this issue:

Fatal error:

umbrella0.tpr: Your pull coordinates have different pull geometry
(coordinate

1: distance, coordinate 2: direction)

If you want to use only some pull coordinates in WHAM, please select them
with

option gmx wham -is


I refer this link to pick one of the two reaction coordiantes to work on
WHAM.
https://urldefense.proofpoint.com/v2/url?u=http-3A__manual.gromacs.org_documentation_2016_onlinehelp_gmx-2Dwham.html=DwIFaQ=nE__W8dFE-shTxStwXtp0A=gCy395jfSTIKIGBjdJ8SwSg8yN7wywRqF0ilx8ZoefpMNPZKIUY0jXzHKcFUwcQV=ylMBZcLbqfFPYBVa5g85k4Po5Oxm2FUPBpXKM3fIYYY=UAqEj3Fxkq5Wq5wgDTU6IGriSSwUWc8o1emqkL1sQ-s=
 

See all the figures in this link:
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.evernote.com_l_AAMsNYa6HXZFeqNDTbsiV4HO0ta2KY-2Dnz7s_=DwIFaQ=nE__W8dFE-shTxStwXtp0A=gCy395jfSTIKIGBjdJ8SwSg8yN7wywRqF0ilx8ZoefpMNPZKIUY0jXzHKcFUwcQV=ylMBZcLbqfFPYBVa5g85k4Po5Oxm2FUPBpXKM3fIYYY=kcFXCPX23_hqHOKeQ3iV61pQ_i0PFkuIsB5K1jKT-Co=
 

When I only selected 'distance' for WHAM, the histogram and PMF looks like
this (Figure 1). I can somewhat understand the insufficient overlap at
0.5-0.75 nm could result in some abnormal segment in PMF, but what really
confused me is the global decreasing on PMF. Then histogram looks just
right.

Here is the result when only selecting 'direction' as the reaction
coordinate for wham (Figure 2). Gromacs's WHAM still output the distance as
x-axis, and the histogram is different form the above one.

Then I just simply add these two PMFs together and got following plots.
(Figure 3) The summation looks like what I expected. I can not understand
this. Because the restraints by 'distance' and 'direction' are
perpendicular to each other, the coordinate-1's WHAM result should be
something like what I got from single reaction coordinate. I expected the
coordinate-1's WHAM result should look like the summation result. I do not
have experience on dealing with two reaction coordinates. So, I will
appreciate it if anybody has suggestions on how to figure this out.

Here is the pulling parameter for my umbrella sampling: Pull code

pull= yes
pull_ngroups= 2  ; there are two pulling groups
pull_ncoords= 2 ; two reaction coordiante to
restraint the molecule around its initial position
pull_group1_name= Other  ; ligand
pull_group2_name= ref_group  . reference group, it is a part of
my peptide
; first reaction coordinate
pull_coord1_type= umbrella  ; harmonic biasing force
pull_coord1_geometry= distance  ; simple distance increase
pull_coord1_groups  = 1 2   ; two groups the pulling will be
applied
pull_coord1_dim = Y Y Y
pull_coord1_rate= 0.0  ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k   = 1000  ; kJ mol^-1 nm^-2
pull_coord1_start   = yes   ; define initial COM distance > 0
; second reaction coordinate
pull_coord2_type= umbrella  ; harmonic biasing force
pull_coord2_geometry= direction  ; simple distance increase
pull_coord2_vec  = 11.018  -20.969  13.824
pull_coord2_groups  = 1 2
pull_coord2_dim = Y Y Y
pull_coord2_rate= 0.0  ; 0.01 nm per ps = 10 nm per ns
pull_coord2_k   = 1000  ; kJ mol^-1 nm^-2
pull_coord2_start   = yes   ; define initial COM distance > 0



Best

Yuanchao Liu (刘元超)
Ph.D. Candidate
Department of Chemical Engineering and Materials Science
428 South Shaw Lane, Room 3263
Michigan State University
East Lansing, Michigan 48824-4437

Email: ycliu1...@gmail.com; liuyu...@msu.edu; liuyu...@egr.msu.edu
Cell:+1 (517)-763-1806
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Re: [gmx-users] How to use the index.ndx when running rms?

[ZHANG Cheng]

Dear All,
After a few tests, I finally got it.


Actually, the command line below does NOT generate a new set of group. 
echo r 1-442 q|gmx make_ndx -f md_0_1.tpr -o index.ndx
Instead, it outputs ALL the 18 groups, each group contains its relevant atom 
numbers.


After reading http://biophysics.med.jhmi.edu/~yliu120/tutorials.html
It says: "If the index file you provide only contains one index group. Then the 
Gromacs program will not ask you for a choice of index groups since you only 
provide one to it."


So I opened my initial .gro file, check the necessary numbers belong to my 
protein. Based on this information, I deleted unnecessary groups and numbers in 
the index.ndx file.


Then run the command with "-n" option:
gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd_noPBC.xvg -tu ns -n index.ndx


And I successfully got the .xvg file.




-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Mon, Aug 14, 2017 11:50 PM
To:  "ZHANG Cheng"<272699...@qq.com>; 
"gromacs.org_gmx-users"; 

Subject:  Re: How to use the index.ndx when running rms?



Hi Justin,
Thank you. I added "-n index.ndx" to my rms command, but still got "Cannot read 
from input" error:


Command line:
  gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd_noPBC.xvg -tu ns -n 
index.ndx


Reading file md_0_1.tpr, VERSION 5.1.1 (single precision)
Reading file md_0_1.tpr, VERSION 5.1.1 (single precision)
Select group for least squares fit
Group 0 ( System) has 127073 elements
Group 1 (Protein) has  8850 elements
Group 2 (  Protein-H) has  4351 elements
Group 3 (C-alpha) has   645 elements
Group 4 (   Backbone) has  1935 elements
Group 5 (  MainChain) has  2785 elements
Group 6 (   MainChain+Cb) has  3194 elements
Group 7 (MainChain+H) has  3816 elements
Group 8 (  SideChain) has  5034 elements
Group 9 (SideChain-H) has  1566 elements
Group10 (Prot-Masses) has  8850 elements
Group11 (non-Protein) has 118223 elements
Group12 (  Water) has 117684 elements
Group13 (SOL) has 117684 elements
Group14 (  non-Water) has  9389 elements
Group15 (Ion) has   539 elements
Group16 ( NA) has   155 elements
Group17 ( CL) has   384 elements
Group18 ( Water_and_ions) has 118223 elements
Select a group: Select a group: Select a group: 
---
Program gmx rms, VERSION 5.1.1
Source code file: 
/dev/shm/tmp.PwtfSrm0uJ/gromacs-5.1.1/src/gromacs/topology/index.cpp, line: 917


Fatal error:
Cannot read from input
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---







-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Mon, Aug 14, 2017 11:09 PM
To:  "gromacs.org_gmx-users"; 
Cc:  "ZHANG Cheng"<272699...@qq.com>; 
Subject:  How to use the index.ndx when running rms?



Dear Gromacs,
After running 
echo r 1-442 q|gmx make_ndx -f md_0_1.tpr -o index.ndx
I got a index.ndx file.


Then I run 
echo 19 19|gmx rms -s md_0_1.tpr -f md_0_1.xtc -o rmsd.xvg -tu ns
But still only 18 options could be recognised. The index.ndx file is already in 
the same folder.


So how to use the index.ndx when running rms?


Thank you.


Yours sincerely
Cheng
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Re: [gmx-users] Recent successful compile on Mac Pro with OpenCL? Failing Test #20: MdrunTests

[Steffen Graether]

Hi Mark,

Thank-you for the suggestion. Not sure if I’ve hit a bit of a circular problem. 
Using Xcode clang and also a brew installed llvm I get this error during cmake:

-- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES) (found 
version "1.0")
-- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES) 
(found version "1.0")
CMake Warning at cmake/gmxManageOpenMP.cmake:70 (message):
  The compiler you are using does not support OpenMP parallelism.  This might
  hurt your performance a lot, in particular with GPUs.  Try using a more
  recent version, or a different compiler.  For now, we are proceeding by
  turning off OpenMP.

Regards,
Steffen

On Aug 14, 2017, at 10:21 AM, Mark Abraham 
> wrote:

Hi,

OK. That might be hard to work out how to fix, because I'm not sure we have
a Mac+AMD machine around. My guess is that somehow the compilation in the
driver assumes the use of xcode compilers, so that might be a thing for you
to try. The file it can't find is one that is installed as part of GROMACS,
but which is in a path that ought to be given to the OpenCL compiler with
-I. Yet somehow that is lost.

Mark

On Mon, Aug 14, 2017 at 2:52 PM Steffen Graether 
>
wrote:

Hi Mark,

Here are the results for a few different runs:

(1) gmx mdrun -v -deffnm md_0_1 -nb cpu
Runs fine and completes

(2) gmx mdrun -v -deffnm md_0_1
Gives a similar error message:
---
Program: gmx mdrun, version 2016.2
Source file: src/gromacs/gpu_utils/ocl_compiler.cpp (line 482)
Function:cl_program gmx::ocl::compileProgram(FILE *, const std::string
&, const std::string &, cl_context, cl_device_id, ocl_vendor_id_t)
MPI rank:0 (out of 2)

Internal error (bug):
Failed to compile NBNXN kernels for GPU #AMD Radeon HD - FirePro D500
Compute
Engine
 Could not build OpenCL program, error was CL_INVALID_BUILD_OPTIONS

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

(3) gmx mdrun -v -deffnm md_0_1 -gpu_id 0
Gives the same as (2)

Regards,
Steffen



 1. Re: Recent successful compile on Mac Pro with OpenCL? Failing
Test #20: MdrunTests (Mark Abraham)


From: Mark Abraham 
mailto:mark.j.abra...@gmail.com>>>
Subject: Re: [gmx-users] Recent successful compile on Mac Pro with OpenCL?
Failing Test #20: MdrunTests
Date: August 14, 2017 at 8:12:38 AM EDT
To: 
gmx-us...@gromacs.org,
 "
gromacs.org_gmx-users@maillist.sys.kth.semailto:gromacs.org_gmx-users@maillist.sys.kth.se>>"
 <
gromacs.org_gmx-users@maillist.sys.kth.semailto:gromacs.org_gmx-users@maillist.sys.kth.se>>>


Hi,

That's a bit mysterious, because we check that that works in our automated
testing. If running a simulation works then everything is fine, but it's
possible the same error arises. Can you try that, please, and report back?

Mark

On Fri, 11 Aug 2017 23:48 Steffen Graether 
mailto:graet...@uoguelph.ca>>> wrote:

Hi,

I am trying to compile GROMACS 2016.3 on a Mac Pro (Late 2013) running
macOS 10.12.6. I can get it to compile fine and it can run my own
simulation fine on CPU only, but I am having difficulty getting to work
with the GPU (FirePro D500).

Used cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=on -DGMX_USE_OPENCL=on
-DREGRESSIONTEST_DOWNLOAD=ON

Tried both clang (version 8) and gcc (version 7), also tried 2016.2 but I
always get this error from Test #20: MdrunTests:

***
Compilation of source file
/Users/graether/Downloads/tmp/gromacs-2016.3/src/gromacs/mdlib/nbnxn_ocl/
nbnxn_ocl_kernels.cl failed!
-- Used build options: -DWARP_SIZE_TEST=64 -D_AMD_SOURCE_
-DGMX_OCL_FASTGEN -DEL_CUTOFF -DEELNAME=_ElecCut -DLJ_COMB_GEOM
-DVDWNAME=_VdwLJCombGeom -DCENTRAL=22
-DNBNXN_GPU_NCLUSTER_PER_SUPERCLUSTER=8 -DNBNXN_GPU_CLUSTER_SIZE=8
-DNBNXN_GPU_JGROUP_SIZE=4 -DNBNXN_MIN_RSQ=3.82e-07f -DIATYPE_SHMEM
-cl-fast-relaxed-math
-I/Users/graether/Downloads/tmp/gromacs-2016.3/src/gromacs/mdlib/nbnxn_ocl
--LOG START---
:61:10: fatal error: 'nbnxn_ocl_kernels.clh' file not found
#include FLAVOR_LEVEL_GENERATOR
   ^
:49:36: note: expanded from macro 'FLAVOR_LEVEL_GENERATOR'
  #define FLAVOR_LEVEL_GENERATOR "nbnxn_ocl_kernels.clh"
 ^
---LOG END

---
Program: mdrun-test, version 2016.3
Source file: src/gromacs/gpu_utils/ocl_compiler.cpp (line 482)
Function:_cl_program* gmx::ocl::compileProgram(FILE*, const string&,
const string&, cl_context, 

Re: [gmx-users] non zero free energy values in mass transformation

[Dan Gil]

Hi Deepak,

I'd like to share a reference with you. http://www.tandfonline.
com/doi/abs/10.1080/00268970600893060

If you could take a look at results (14) versus (15), and results (28)
versus (29)... You see that when only the potential energy is considered,
the mass doesn't contribute to the free energy. However this is based on
the assumption that the mass between the two states are equal. The mass
between Li+ and Cl- are rather different.

Please correct me if I am wrong, but I believe TPI compares between two
states, a solute in the ideal gas phase and the same solute in water (in
your case). E.g. [Li]_idealGas -> [Li]_aqueous. The mass is not changing
here.

On the other hand TI considers two states with different species. In your
case, it is [Li]_aqueous -> [Cl]_aqueous. The two states being compared is
different than TPI. In TI, the masses of the solutes are different. I think
the idea is that when you do a TI in water and do a TI in gas, the mass
contributions to the free energy cancel out. Can you also try doing
[Li]_idealGas -> [Cl]_idealGas? Hopefully, the free energy change due to
the mass perturbation for the two transformations cancel out to zero.

A disclaimer though, I am also working on a very similar problem without
success (yet). I am very curious to see if this works out for you.

Dan


On Sun, Aug 13, 2017 at 11:08 PM, deepak bapat  wrote:

> Hi
>
> To study the efect of particle mass on excess chemical potential i did test
> particle insertion  (tpi) in SPC/E water. I created a lennard jones
> particle with very small LJ parameters so that the probability of gettining
> it inside the cavity increases.
>
> In one case I kept mass of tpi particle equal to that of Lithium. In second
> simulation the mass was equal to that of Chlorine atome.
>
> LJ parameters for tpi particles in both cases were 2.0e-02  7.64793e-02.
>
> In both cases the excess chemical potential was in the range of 0.0798
> kJ/mol.
>
> tpi only considers energy as a function of coordinates only so i assume
> that it would depend only on LJ parameters as long as we are delaing with
> neutral systems.
>
> So looking at this I again come back to the mass perturbation which started
> all this.
>
> Since I was doing NPT calculations at 300 K I expected that average total
> kinetic energy of the system should not be different. The themostat would
> just adjust velocity distribution so that it brings the temperature of the
> system to the set temperature. Any increase or decrease in mass should be
> accounted for by the thermostat.
>
> As I said, in free energy calculations I got non zero value. (~ +6.2
> kJ/mol). So I am still worried about this non zero behavior.
>
> Thanks and regards
>
> Deepak
>
>
>
>
>
>
>
>
>
>
>
> On Sat, Aug 12, 2017 at 10:11 AM, deepak bapat  wrote:
>
> > Thank you Andre and Dan.
> >
> > I'll read more about.
> >
> > Deepak
> >
> > On Fri, Aug 11, 2017 at 7:35 PM, Dan Gil  wrote:
> >
> >> Hi Deepak,
> >>
> >> I am battling the same problem too. I am doing free energy calculation
> for
> >> heptane -> perfluoro-heptane in water. Also SPC/E water, Gromacs 5.1.
> >>
> >> Like Andre said, there is expected to be a free energy change when you
> >> change the mass of a particle. But if you do the same transformation
> from
> >> Li+ to Cl- in the gas phase, hopefully the free energy change will be
> >> opposite and (approximately) equal. Have you tried doing this second
> >> calculation [Li+ -> Cl-] in the gas phase? I think this website:
> >> http://www.alchemistry.org/wiki/Thermodynamic_Cycle explains why this
> >> second step might be needed better.
> >>
> >> Dan
> >>
> >> On Fri, Aug 11, 2017 at 9:37 AM, André Farias de Moura  >
> >> wrote:
> >>
> >> > Deepak,
> >> >
> >> > I never did a mass perturbation myself, but I would expect some free
> >> energy
> >> > change, since the translational partition function depends on the mass
> >> of
> >> > the molecules.
> >> >
> >> > Also, having the same kinetic energy is not meaningful at all, the
> >> correct
> >> > quantity you should always use in statistical mechanics reasoning is
> the
> >> > momentum of the particle, p=mv, which clearly changes during your
> >> > alchemical transformation. Put in another way: the phase space of the
> >> > system is a 6N dimensional space of positions and momenta, and you
> have
> >> > just perturbed the momenta part.
> >> >
> >> > And by the way: that is a typical case in which Monte Carlo methods
> >> would
> >> > fail to reproduce an MD result, since only the configurational phase
> >> space
> >> > is sampled in MC (masses effects would have to be added afterwards,
> >> > assuming that some analytical result could be computed)
> >> >
> >> > I hope it helps
> >> >
> >> > Andre
> >> >
> >> > On Fri, Aug 11, 2017 at 6:36 AM, deepak bapat 
> >> wrote:
> >> >
> >> > > Dear Gmx Users
> >> > >
> >> > > I am trying to find out 

Re: [gmx-users] How to use the index.ndx when running rms?

[Justin Lemkul]

On 8/14/17 11:09 AM, ZHANG Cheng wrote:

Dear Gromacs,
After running
echo r 1-442 q|gmx make_ndx -f md_0_1.tpr -o index.ndx
I got a index.ndx file.


Then I run
echo 19 19|gmx rms -s md_0_1.tpr -f md_0_1.xtc -o rmsd.xvg -tu ns
But still only 18 options could be recognised. The index.ndx file is already in 
the same folder.


So how to use the index.ndx when running rms?

If you don't tell gmx rms to use the index (via -n), it won't.

-Justin

--
==

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

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

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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[gmx-users] How to use the index.ndx when running rms?

[ZHANG Cheng]

Dear Gromacs,
After running 
echo r 1-442 q|gmx make_ndx -f md_0_1.tpr -o index.ndx
I got a index.ndx file.


Then I run 
echo 19 19|gmx rms -s md_0_1.tpr -f md_0_1.xtc -o rmsd.xvg -tu ns
But still only 18 options could be recognised. The index.ndx file is already in 
the same folder.


So how to use the index.ndx when running rms?


Thank you.


Yours sincerely
Cheng
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Re: [gmx-users] Recent successful compile on Mac Pro with OpenCL? Failing Test #20: MdrunTests

[Mark Abraham]

Hi,

OK. That might be hard to work out how to fix, because I'm not sure we have
a Mac+AMD machine around. My guess is that somehow the compilation in the
driver assumes the use of xcode compilers, so that might be a thing for you
to try. The file it can't find is one that is installed as part of GROMACS,
but which is in a path that ought to be given to the OpenCL compiler with
-I. Yet somehow that is lost.

Mark

On Mon, Aug 14, 2017 at 2:52 PM Steffen Graether 
wrote:

> Hi Mark,
>
> Here are the results for a few different runs:
>
> (1) gmx mdrun -v -deffnm md_0_1 -nb cpu
> Runs fine and completes
>
> (2) gmx mdrun -v -deffnm md_0_1
> Gives a similar error message:
> ---
> Program: gmx mdrun, version 2016.2
> Source file: src/gromacs/gpu_utils/ocl_compiler.cpp (line 482)
> Function:cl_program gmx::ocl::compileProgram(FILE *, const std::string
> &, const std::string &, cl_context, cl_device_id, ocl_vendor_id_t)
> MPI rank:0 (out of 2)
>
> Internal error (bug):
> Failed to compile NBNXN kernels for GPU #AMD Radeon HD - FirePro D500
> Compute
> Engine
>   Could not build OpenCL program, error was CL_INVALID_BUILD_OPTIONS
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> (3) gmx mdrun -v -deffnm md_0_1 -gpu_id 0
> Gives the same as (2)
>
> Regards,
> Steffen
>
>
>
>   1. Re: Recent successful compile on Mac Pro with OpenCL? Failing
>  Test #20: MdrunTests (Mark Abraham)
>
>
> From: Mark Abraham >
> Subject: Re: [gmx-users] Recent successful compile on Mac Pro with OpenCL?
> Failing Test #20: MdrunTests
> Date: August 14, 2017 at 8:12:38 AM EDT
> To: gmx-us...@gromacs.org, "
> gromacs.org_gmx-users@maillist.sys.kth.se gromacs.org_gmx-users@maillist.sys.kth.se>" <
> gromacs.org_gmx-users@maillist.sys.kth.se gromacs.org_gmx-users@maillist.sys.kth.se>>
>
>
> Hi,
>
> That's a bit mysterious, because we check that that works in our automated
> testing. If running a simulation works then everything is fine, but it's
> possible the same error arises. Can you try that, please, and report back?
>
> Mark
>
> On Fri, 11 Aug 2017 23:48 Steffen Graether > wrote:
>
> Hi,
>
> I am trying to compile GROMACS 2016.3 on a Mac Pro (Late 2013) running
> macOS 10.12.6. I can get it to compile fine and it can run my own
> simulation fine on CPU only, but I am having difficulty getting to work
> with the GPU (FirePro D500).
>
> Used cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=on -DGMX_USE_OPENCL=on
> -DREGRESSIONTEST_DOWNLOAD=ON
>
> Tried both clang (version 8) and gcc (version 7), also tried 2016.2 but I
> always get this error from Test #20: MdrunTests:
>
> ***
> Compilation of source file
> /Users/graether/Downloads/tmp/gromacs-2016.3/src/gromacs/mdlib/nbnxn_ocl/
> nbnxn_ocl_kernels.cl failed!
> -- Used build options: -DWARP_SIZE_TEST=64 -D_AMD_SOURCE_
> -DGMX_OCL_FASTGEN -DEL_CUTOFF -DEELNAME=_ElecCut -DLJ_COMB_GEOM
> -DVDWNAME=_VdwLJCombGeom -DCENTRAL=22
> -DNBNXN_GPU_NCLUSTER_PER_SUPERCLUSTER=8 -DNBNXN_GPU_CLUSTER_SIZE=8
> -DNBNXN_GPU_JGROUP_SIZE=4 -DNBNXN_MIN_RSQ=3.82e-07f -DIATYPE_SHMEM
> -cl-fast-relaxed-math
> -I/Users/graether/Downloads/tmp/gromacs-2016.3/src/gromacs/mdlib/nbnxn_ocl
> --LOG START---
> :61:10: fatal error: 'nbnxn_ocl_kernels.clh' file not found
> #include FLAVOR_LEVEL_GENERATOR
> ^
> :49:36: note: expanded from macro 'FLAVOR_LEVEL_GENERATOR'
>#define FLAVOR_LEVEL_GENERATOR "nbnxn_ocl_kernels.clh"
>   ^
> ---LOG END
>
> ---
> Program: mdrun-test, version 2016.3
> Source file: src/gromacs/gpu_utils/ocl_compiler.cpp (line 482)
> Function:_cl_program* gmx::ocl::compileProgram(FILE*, const string&,
> const string&, cl_context, cl_device_id, ocl_vendor_id_t)
>
> Internal error (bug):
> Failed to compile NBNXN kernels for GPU #AMD Radeon HD - FirePro D500
> Compute
> Engine
>  Could not build OpenCL program, error was CL_BUILD_PROGRAM_FAILURE
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> **
>
> All the other tests are successful.
>
> Regards,
> Steffen
>
>
> --
>
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Re: [gmx-users] NVT error

[Justin Lemkul]

Please don't reply to the entire digest, and be sure to change the 
subject line.


On 8/14/17 9:51 AM, Faez Iqbal Khan wrote:

Dear Justin,

I talk to administrator
They said:

"Dear Faez,

I picked this up in your error file:

There is no domain decomposition for 105 ranks that is compatible with the
given box and a minimum cell size of 1.025 nm
Change the number of ranks or mdrun option -rcon or -dds or your LINCS
settings
Look in the log file for details on the domain decomposition"

Have you tried Googling this error?  People ask about it all the time.

The short answer is that you have to determine an appropriate number of 
ranks over which to parallelize your system.  You can't just arbitrarily 
parallelize over any number of ranks/cores.  Your system is much too 
small to use so many ranks.


-Justin

--
==

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

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

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] Donors and Acceptors - gmx hbond - gromacs.org_gmx-users Digest, Vol 160, Issue 67

[Marcelo Depólo]

Hi Mark,


I've tried your suggestion. I've made an index file with my oxygen (O) and
my hydroxyl group (OH). Here my results:

H-bond average (calculated using num.xvg):
O = 1.10 +/- 0.62
OH = 2.06 +/- 0.66

(The first line from .log for each group)
# DonorHydrogen  Acceptor
O=  SOL2OW  SOL2HW1  MET1O
OH =   MET1O MET1HHSOL2OW

My command line for each group was:

gmx_507 hbond -s met.SIM.tpr -f met.SIM-traj.xtc -n wat_ana.ndx -shell 0.5
-r 0.35 -a 30 -num met.num.xvg -hbn met.hbn.ndx -don met.donors.xvg -dan
met.dan.xvg -g met.log

So I am a bit confused. I was expecting only 1 H-bond from OH group (since
O is able to donate only one H), and 2 H-bonds accepted for O. Based on the
.log, gmx hbond doesn't seem to be calculating H-bond for acceptors and
donors at the same time, what would justify this value of 2 for OH (1
accepted and 1 donated).

So, I ran out of ideas. Does anyone have any? Does these values make sense?

Cheers!
Marcelo

--
>
> Message: 2
> Date: Mon, 14 Aug 2017 12:13:38 +
> From: Mark Abraham 
> To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] Donors and Acceptors - gmx hbond
> Message-ID:
>  mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
>
> I would use the selection groups judiciously, for example have one of them
> with only donor atoms in it.
>
> Mark
>
>
-- 
--
Marcelo Depólo Polêto
DSc. Cell and Molecular Biology - UFRGS (Brazil)
Group of Structural Bioinformatics - Room 202
Center of Biotechnology - UFRGS
Phone: + 55 51 3308-7770
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 160, Issue 63

[Faez Iqbal Khan]

Dear Justin,

I talk to administrator
They said:

"Dear Faez,

I picked this up in your error file:

There is no domain decomposition for 105 ranks that is compatible with the
given box and a minimum cell size of 1.025 nm
Change the number of ranks or mdrun option -rcon or -dds or your LINCS
settings
Look in the log file for details on the domain decomposition"

Can you please suggest, how to use thes commands.

Thanks

On Sun, Aug 13, 2017 at 10:31 PM, <
gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:

> Send gromacs.org_gmx-users mailing list submissions to
> gromacs.org_gmx-users@maillist.sys.kth.se
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or, via email, send a message with subject or body 'help' to
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>
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>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gromacs.org_gmx-users digest..."
>
>
> Today's Topics:
>
>1. Re: NVT error (Justin Lemkul)
>2. Re: Magic Number Error in XTC file (read 0, should be 1995)
>   (Justin Lemkul)
>3. Re: ligand (farial tavakoli)
>4. Re: ligand (Justin Lemkul)
>5. Difference in omega angles!! (Seera Suryanarayana)
>6. Re: Difference in omega angles!! (Justin Lemkul)
>
>
> --
>
> Message: 1
> Date: Sun, 13 Aug 2017 13:11:39 -0400
> From: Justin Lemkul 
> To: Discussion list for GROMACS users 
> Subject: Re: [gmx-users] NVT error
> Message-ID: <5b2aa8f8-1873-3983-0be3-143eb12e5...@vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 8/13/17 12:45 PM, Faez Iqbal Khan wrote:
> > Hi
> > I am running MD simulation of Pro-Lig complex using protocol provided by
> Justin
> > Lemkul.
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
> gmx-tutorials/complex/06_equil.html
> >  bevanlab.biochem.vt.edu%2FPages%2FPersonal%2Fjustin%
> 2Fgmx-tutorials%2Fcomplex%2F06_equil.html>
> >
> > I am getting error at NVT stage.
> >
> > I am attaching my log files. Please suggest. Many many Thanks
>
> I don't see any error message, it just looks like your run hung.  Talk to
> your
> system administrator about proper usage and/or compilation.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
>
> --
>
> Message: 2
> Date: Sun, 13 Aug 2017 13:12:43 -0400
> From: Justin Lemkul 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Magic Number Error in XTC file (read 0,
> should be 1995)
> Message-ID: <2af71571-a1cc-0ee9-cd45-7a86d4ae0...@vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 8/13/17 12:47 PM, ZHANG Cheng wrote:
> > Hi Justin,
> > Thank you for explaining that.
> >
> >
> > You said "a more reliable system", what does this mean? It is my first
> time adding glycines to my protein using OPLS-AA/L force field. Do you
> think this might be the reason, and should I switch to another force field?
> >
>
> I'm talking about hardware.  Failure to write a valid frame is usually due
> to a
> filesystem problem (i.e. hard disk).  It doesn't matter what your force
> field is
> or what your system contents are.
>
> >
> > My procedure is as follows:
> > 1) I get the glycine and protein pdb, convert them to .gro files using
> > gmx pdb2gmx -f glycine/protein.pdb -o glycine/protein.gro -water spce
> -inter
> > 2) then I add the protein.gro into a box, get the protein_newbox.gro:
> > gmx editconf -f protein.gro -o protein_newbox.gro -c -d 1.0 -bt cubic
> > 3) then I add glycines to this box:
> > gmx insert-molecules -ci glycine.gro -nmol 203 -f protein_newbox.gro -o
> protein_203_glycine.gro
> > 4) then I do the exactly the same thing according to your tutorial, i.e.
> solvent with water, add ions, energy minimization, NVT, NPT, and finally
> the MD.
> >
> >
> > Can I ask if the procedure is correct? Would you please recommend some
> tutorial for prepare a system with protein and excipients (e.g. glycine,
> sorbitol, etc)?
> >
>
> It's fine.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>

Re: [gmx-users] ligand

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }   Dear justin
Thank you so much 
Yours sincerelyFarial


Sent from Yahoo Mail for iPhone


On Monday, August 14, 2017, 4:35 PM, Justin Lemkul  wrote:



On 8/14/17 2:03 AM, ‪farial tavakoli‬ ‪ wrote:
> Dear Justin
> Thanks for your advice.Now I am trying to create a .gro file from the united 
> atom pdb structure file obtained from ATB  by using :editconf -f xxx.pdb -o 
> xxx.gro
> but faced to this warning:
> WARNING: all CONECT records are ignored
> would you please advice me how can i solve this problem?

You don't.  You don't need connectivity information from the PDB because 
it's all in the topology.  This really shouldn't be a "warning," rather 
an informative note.

-Justin

-- 
==

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

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

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] Problem with Ryzen, threads and core dumps?

[Steffen Graether]

Hi everyone,

I had some time on the weekend to try to troubleshoot this. Updating the BIOS 
and trying different compilers didn’t help, but updating the kernel to 4.11.12 
has made for a much more stable system. I ran a 1 ns five times and it only 
crashed once.

Regards,
Steffen

> On Aug 8, 2017, at 6:03 PM, Steffen Graether  wrote:
> 
> Hi,
> 
> I am trying to run a protein/water simulation using a new computer (Ryzen 
> 1700X, Nvidia GTX 1070 running Ubuntu 17.04). I compiled GROMACS 2016.3 with 
> gcc-5 (CUDA 8.0 complained that it only supports up to version 5) and 
> -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON, otherwise defaults were 
> used. The build passed all make check tests.
> 
> During the production mdrun, I would get core dumps almost all of the time 
> (mostly segmentation faults, sometimes illegal instructions, once it actually 
> completed the 1 ps run). I also tried different water (TIP4P2005 and SPCE), 
> but no change. I haven’t tried a different forcefield yet (just Amber 
> ff03WS), but feel like that isn’t the problem.
> 
> Suggestions I found online seem to be mostly about not having compiled gmx on 
> the current machine, which I had done. I also tried recompiling with SSE4.1, 
> but still got a core dump. Interestingly restricting the program to the 
> number of physical cores (-nt 8) lets the run complete more often (3/4 
> attempts), but still crash.
> 
> I would be appreciative of any suggestions people may have for compiling a 
> more stable executable.
> 
> Thanks,
> Steffen

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Re: [gmx-users] Recent successful compile on Mac Pro with OpenCL? Failing Test #20: MdrunTests

[Steffen Graether]

Hi Mark,

Here are the results for a few different runs:

(1) gmx mdrun -v -deffnm md_0_1 -nb cpu
Runs fine and completes

(2) gmx mdrun -v -deffnm md_0_1
Gives a similar error message:
---
Program: gmx mdrun, version 2016.2
Source file: src/gromacs/gpu_utils/ocl_compiler.cpp (line 482)
Function:cl_program gmx::ocl::compileProgram(FILE *, const std::string &, 
const std::string &, cl_context, cl_device_id, ocl_vendor_id_t)
MPI rank:0 (out of 2)

Internal error (bug):
Failed to compile NBNXN kernels for GPU #AMD Radeon HD - FirePro D500 Compute
Engine
  Could not build OpenCL program, error was CL_INVALID_BUILD_OPTIONS

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

(3) gmx mdrun -v -deffnm md_0_1 -gpu_id 0
Gives the same as (2)

Regards,
Steffen



  1. Re: Recent successful compile on Mac Pro with OpenCL? Failing
 Test #20: MdrunTests (Mark Abraham)


From: Mark Abraham >
Subject: Re: [gmx-users] Recent successful compile on Mac Pro with OpenCL? 
Failing Test #20: MdrunTests
Date: August 14, 2017 at 8:12:38 AM EDT
To: gmx-us...@gromacs.org, 
"gromacs.org_gmx-users@maillist.sys.kth.se"
 
>


Hi,

That's a bit mysterious, because we check that that works in our automated
testing. If running a simulation works then everything is fine, but it's
possible the same error arises. Can you try that, please, and report back?

Mark

On Fri, 11 Aug 2017 23:48 Steffen Graether 
> wrote:

Hi,

I am trying to compile GROMACS 2016.3 on a Mac Pro (Late 2013) running
macOS 10.12.6. I can get it to compile fine and it can run my own
simulation fine on CPU only, but I am having difficulty getting to work
with the GPU (FirePro D500).

Used cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=on -DGMX_USE_OPENCL=on
-DREGRESSIONTEST_DOWNLOAD=ON

Tried both clang (version 8) and gcc (version 7), also tried 2016.2 but I
always get this error from Test #20: MdrunTests:

***
Compilation of source file
/Users/graether/Downloads/tmp/gromacs-2016.3/src/gromacs/mdlib/nbnxn_ocl/
nbnxn_ocl_kernels.cl failed!
-- Used build options: -DWARP_SIZE_TEST=64 -D_AMD_SOURCE_
-DGMX_OCL_FASTGEN -DEL_CUTOFF -DEELNAME=_ElecCut -DLJ_COMB_GEOM
-DVDWNAME=_VdwLJCombGeom -DCENTRAL=22
-DNBNXN_GPU_NCLUSTER_PER_SUPERCLUSTER=8 -DNBNXN_GPU_CLUSTER_SIZE=8
-DNBNXN_GPU_JGROUP_SIZE=4 -DNBNXN_MIN_RSQ=3.82e-07f -DIATYPE_SHMEM
-cl-fast-relaxed-math
-I/Users/graether/Downloads/tmp/gromacs-2016.3/src/gromacs/mdlib/nbnxn_ocl
--LOG START---
:61:10: fatal error: 'nbnxn_ocl_kernels.clh' file not found
#include FLAVOR_LEVEL_GENERATOR
^
:49:36: note: expanded from macro 'FLAVOR_LEVEL_GENERATOR'
   #define FLAVOR_LEVEL_GENERATOR "nbnxn_ocl_kernels.clh"
  ^
---LOG END

---
Program: mdrun-test, version 2016.3
Source file: src/gromacs/gpu_utils/ocl_compiler.cpp (line 482)
Function:_cl_program* gmx::ocl::compileProgram(FILE*, const string&,
const string&, cl_context, cl_device_id, ocl_vendor_id_t)

Internal error (bug):
Failed to compile NBNXN kernels for GPU #AMD Radeon HD - FirePro D500
Compute
Engine
 Could not build OpenCL program, error was CL_BUILD_PROGRAM_FAILURE

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
**

All the other tests are successful.

Regards,
Steffen


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Re: [gmx-users] Can I specify the residue numbers for RMSD?

[Justin Lemkul]

On 8/14/17 8:15 AM, ZHANG Cheng wrote:

Dear Gromacs,
My MD contains a protein (442 residues) and 203 free glycines. The numbering of 
the residues is:


1-442: the protein residues
443-645: the 203 free glycines


When I use the "rms" command, all the 645 residues are considered as the 
"Protein" category.


I cannot find an option that could only calculate rmsd for the first 442 
residues in my proteins. How can I do this? Thank you.


Create an index group with gmx make_ndx or gmx select.

-Justin



Group 0 ( System)
Group 1 (Protein)
Group 2 (  Protein-H)
Group 3 (C-alpha)
Group 4 (   Backbone)
Group 5 (  MainChain)
Group 6 (   MainChain+Cb)
Group 7 (MainChain+H)
Group 8 (  SideChain)
Group 9 (SideChain-H)
Group10 (Prot-Masses)
Group11 (non-Protein)
Group12 (  Water)
Group13 (SOL)
Group14 (  non-Water)
Group15 (Ion)
Group16 ( NA)
Group17 ( CL)
Group18 ( Water_and_ions)


--
==

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303 Engel Hall
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Re: [gmx-users] Potential Shift Verlet

[Mark Abraham]

Hi,

I don't think so, because it's trivial - it's defined as the value of the
potential at the distance of the cutoff.

Mark

On Thu, 10 Aug 2017 19:44 Natalie Paige Schieber <
natalie.schie...@colorado.edu> wrote:

> Hi all,
>
> I am using the potential-shift-verlet keyword for the coulomb-modifier. I
> am attempting to find the specific equation for this treatment of the
> electrostatics. In the manual for the most recent version of Gromacs I
> found an equation for potential-switch (eq 4.30) but not shift. Is there
> somewhere I can find the corresponding equation for potential-shift?
>
> Thanks,
> Natalie
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Re: [gmx-users] Donors and Acceptors - gmx hbond

[Mark Abraham]

Hi,

I would use the selection groups judiciously, for example have one of them
with only donor atoms in it.

Mark

On Fri, 11 Aug 2017 00:05 Marcelo Depólo  wrote:

> Hi all!
>
>
> I've been wondering how donors and acceptors are defined in gmx hbond. In
> the help output:
>
> "(...) OH and NH groups are regarded as donors, O is an acceptor always, N
> is an acceptor by default, but this can be switched using -nitacc. Dummy
> hydrogen atoms are assumed to be connected to the first  preceding
> non-hydrogen atom.
>
> You need to specify two groups for analysis, which must be either identical
> or
> non-overlapping. All hydrogen bonds between the two groups are analyzed."
>
> So if I evaluate a 'OH' group (in MeOH - water solution, for example), will
> I be calculating the h-bonds donated by H atom and accepted by the O atom
> at the same time? If so, is there anyway to calculate both separately?
>
> Cheers!
> --
> Marcelo Depólo Polêto
> DSc. Cell and Molecular Biology - UFRGS (Brazil)
> Group of Structural Bioinformatics - Room 202
> Center of Biotechnology - UFRGS
> Phone: + 55 51 3308-7770
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Re: [gmx-users] Recent successful compile on Mac Pro with OpenCL? Failing Test #20: MdrunTests

[Mark Abraham]

Hi,

That's a bit mysterious, because we check that that works in our automated
testing. If running a simulation works then everything is fine, but it's
possible the same error arises. Can you try that, please, and report back?

Mark

On Fri, 11 Aug 2017 23:48 Steffen Graether  wrote:

> Hi,
>
> I am trying to compile GROMACS 2016.3 on a Mac Pro (Late 2013) running
> macOS 10.12.6. I can get it to compile fine and it can run my own
> simulation fine on CPU only, but I am having difficulty getting to work
> with the GPU (FirePro D500).
>
> Used cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=on -DGMX_USE_OPENCL=on
> -DREGRESSIONTEST_DOWNLOAD=ON
>
> Tried both clang (version 8) and gcc (version 7), also tried 2016.2 but I
> always get this error from Test #20: MdrunTests:
>
> ***
> Compilation of source file
> /Users/graether/Downloads/tmp/gromacs-2016.3/src/gromacs/mdlib/nbnxn_ocl/
> nbnxn_ocl_kernels.cl failed!
> -- Used build options: -DWARP_SIZE_TEST=64 -D_AMD_SOURCE_
> -DGMX_OCL_FASTGEN -DEL_CUTOFF -DEELNAME=_ElecCut -DLJ_COMB_GEOM
> -DVDWNAME=_VdwLJCombGeom -DCENTRAL=22
> -DNBNXN_GPU_NCLUSTER_PER_SUPERCLUSTER=8 -DNBNXN_GPU_CLUSTER_SIZE=8
> -DNBNXN_GPU_JGROUP_SIZE=4 -DNBNXN_MIN_RSQ=3.82e-07f -DIATYPE_SHMEM
> -cl-fast-relaxed-math
> -I/Users/graether/Downloads/tmp/gromacs-2016.3/src/gromacs/mdlib/nbnxn_ocl
> --LOG START---
> :61:10: fatal error: 'nbnxn_ocl_kernels.clh' file not found
> #include FLAVOR_LEVEL_GENERATOR
>  ^
> :49:36: note: expanded from macro 'FLAVOR_LEVEL_GENERATOR'
> #define FLAVOR_LEVEL_GENERATOR "nbnxn_ocl_kernels.clh"
>^
> ---LOG END
>
> ---
> Program: mdrun-test, version 2016.3
> Source file: src/gromacs/gpu_utils/ocl_compiler.cpp (line 482)
> Function:_cl_program* gmx::ocl::compileProgram(FILE*, const string&,
> const string&, cl_context, cl_device_id, ocl_vendor_id_t)
>
> Internal error (bug):
> Failed to compile NBNXN kernels for GPU #AMD Radeon HD - FirePro D500
> Compute
> Engine
>   Could not build OpenCL program, error was CL_BUILD_PROGRAM_FAILURE
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> **
>
> All the other tests are successful.
>
> Regards,
> Steffen
>
>
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Re: [gmx-users] PBC ISSUES IN GROMACS

[Mark Abraham]

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
had useful information

Mark

On Mon, 14 Aug 2017 09:17 Neha Gupta  wrote:

> Hi gromacs users,
>
> After simulation for 5 ns, I generated a movie.pdb file using .gro and .xtc
>
> However, in the movie file, I witnessed bizarre long bonds...
>
> How to fix it?
>
> Any suggestions please?
>
>
> Thanks,
> Neha
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Re: [gmx-users] ligand

[Justin Lemkul]

On 8/14/17 2:03 AM, ‪farial tavakoli‬ ‪ wrote:

Dear Justin
Thanks for your advice.Now I am trying to create a .gro file from the united 
atom pdb structure file obtained from ATB  by using :editconf -f xxx.pdb -o 
xxx.gro
but faced to this warning:
WARNING: all CONECT records are ignored
would you please advice me how can i solve this problem?


You don't.  You don't need connectivity information from the PDB because 
it's all in the topology.  This really shouldn't be a "warning," rather 
an informative note.


-Justin

--
==

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

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

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[gmx-users] Drift with groups+tabulated potential.

[sperez14]

Dear GROMACS Community, 

I am trying to do a simulation using a tabulated potential which forces
me to use the group cut-off. I get a drift in the conserved quantity of
-600KJ/mol/ns. My system consists of 1000 rigid TIP4P water molecules
and a Na+ ion. It seems that the problem is in the group cut-off since
when I change the tabulated potential for a regular vdw the problem
persists. I have followed the instructions of:  

 http://www.gromacs.org/@api/deki/files/94/=gromacs_nb.pdf 

Is this the kind of energy drift acceptable? I include a copy of the
.mdp file. 

Thanks for your help, 

Sergio  

integrator = md 
dt = 0.001 
nsteps = 10 
init-step = 0   
cutoff-scheme = group  
nst-list = 1  
verlet-buffer-tolerance = 0.0005 
ns-type = grid 
rlist = 1.3 
pbc = xyz 
coulombtype = PME-switch  
rcoulomb = 1.  
rcoulomb-switch = 0.95  
pme-order =  4 
fourierspacing =  0.1 
ewald-rtol = 1.e-5  
vdwtype = user   
rvdw = 1.0  
DispCorr = No 
tcoupl = v-rescale 
tc-grps = System 
;nsttcouple = 1 
tau-t = ref-t = 300.0  
constraints = all-angles 
constraint-algorithm = LINCS 
lincs_iter  = 1  
lincs_order = 4  
energygrps = NA OW 
energygrp_table = NA OW 
comm-mode = linear
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Re: [gmx-users] PBC ISSUES IN GROMACS

[David van der Spoel]

On 14/08/17 09:17, Neha Gupta wrote:

Hi gromacs users,

After simulation for 5 ns, I generated a movie.pdb file using .gro and .xtc

However, in the movie file, I witnessed bizarre long bonds...

How to fix it?

Any suggestions please?

trjconv -pbc whole



Thanks,
Neha




--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
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[gmx-users] PBC ISSUES IN GROMACS

[Neha Gupta]

Hi gromacs users,

After simulation for 5 ns, I generated a movie.pdb file using .gro and .xtc

However, in the movie file, I witnessed bizarre long bonds...

How to fix it?

Any suggestions please?


Thanks,
Neha
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Re: [gmx-users] ligand

[‪farial tavakoli‬ ‪]

Dear Justin
Thanks for your advice.Now I am trying to create a .gro file from the united 
atom pdb structure file obtained from ATB  by using :editconf -f xxx.pdb -o 
xxx.gro
but faced to this warning:
WARNING: all CONECT records are ignored
would you please advice me how can i solve this problem?
thanks alotFarial

  From: Justin Lemkul 
 To: gmx-us...@gromacs.org 
 Sent: Sunday, 13 August 2017, 21:45:53
 Subject: Re: [gmx-users] ligand
   


On 8/13/17 12:29 PM, farial tavakoli wrote:
>  blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
>#715FFA solid !important; padding-left:1ex !important; background-color:white 
>!important; }  Dear justin
> Thank you for your replyI thought that topology file obtained from ATB needs 
> to be changed like PRODRG
> 

No, they generally should not.  ATB is a much better topology source than 
PRODRG.  That doesn't necessarily mean you should always trust a black box 
without some validation, but you shouldn't just blindly go messing with things 
because some other program is known to be problematic.

-Justin

-- 
==

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

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

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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