[gmx-users] Segfaults when using Replica Exchange

[Thomas Allen]

I'm having an issue where GROMACS is generating segfaults when I try  
to run replica exchange simulations on a system of ~300,000 atoms  
using 20 temperature points and around 10,000 cores. This happens when  
using either the 2016.3 version or the 5.1.2 version of the code, and  
I've tried varying the number of cores a bit and turning off dynamic  
load balancing so far, but neither of these things prevent it from  
eventually encountering this error. I have been able to run much  
smaller REMD simulations of the same model, and I can run regular MD  
on it successfully, but I would like to use replica exchange for the  
production calculations to improve my sampling.


I haven't had much luck debugging this through the sysadmins on the  
computing side so I was wondering if anyone was aware of what might be  
causing the trouble on the GROMACS end. I did see some old bug reports  
for version 4 regarding similar issues but my understanding was that  
these had been fixed.


Thanks,
Tom


--
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.

Re: [gmx-users] GMX 2018 regression tests: cufftPlanMany R2C plan failure (error code 5)

[Alex]

And this is with:
> gcc --version
> gcc (Ubuntu 5.4.0-6ubuntu1~16.04.6) 5.4.0 20160609



On Tue, Feb 6, 2018 at 1:18 PM, Alex  wrote:

> Hi all,
>
> I've just built the latest version and regression tests are running. Here
> is one error:
>
> "Program: mdrun-test, version 2018
> Source file: src/gromacs/ewald/pme-3dfft.cu (line 56)
>
> Fatal error:
> cufftPlanMany R2C plan failure (error code 5)"
>
> This is with CUDA 9.1.
>
> Anything to worry about?
>
> Thank you,
>
> Alex
>
-- 
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.

[gmx-users] GMX 2018 regression tests: cufftPlanMany R2C plan failure (error code 5)

[Alex]

Hi all,

I've just built the latest version and regression tests are running. Here
is one error:

"Program: mdrun-test, version 2018
Source file: src/gromacs/ewald/pme-3dfft.cu (line 56)

Fatal error:
cufftPlanMany R2C plan failure (error code 5)"

This is with CUDA 9.1.

Anything to worry about?

Thank you,

Alex
-- 
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.

Re: [gmx-users] pdb2gmx "dangling bond" error when trying to make periodically connected DNA

[Viveca Lindahl]

Hi again,

It seems from previous posts that this type of system setup is of general
interest so I thought I'd share the solution(s).

I modified the tdb file for the 5' end, here for CHARMM27, by adding the
following to the end of dna.n.tdb

[ hack ]
[ replace ]
C5' C5' CN8B12.011 -0.08

Then in pdb2gmx -ter I choose 'hack' as the 5' terminal end. This gives the
C5' atom in the pdb file atomtype CN8B with charge -08 (which is the same
type and charge it would get if it was a non-terminal residue). For the 3'
end I choose 'none'.

Honestly, I don't know why it works -- looks like there still are "dangling
bonds" at both ends. But it seems to do the trick. The output looks like
what I want and no fatal errors. I think I'm just lucky in evading the
fatal error somehow. Another way to accomplish the same thing is to
recompile gmx with the fatal errors commented out.



Viveca

On Fri, Feb 2, 2018 at 5:21 PM, Viveca Lindahl 
wrote:

> Hi,
>
> I'm trying to create a topology for DNA with periodically connected ends.
> There's a previous message on this, with advice by Justin:
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_
> gmx-users/2015-April/096970.html
>
> I have a single-stranded DNA structure in a pdb file with a phosphate on
> one end (P, OP1, OP2) and an oxygen on the other (O3'). These are exactly
> the atoms I want to connect later on. I use pdb2gmx to get the hydrogens +
> topology and give it -ter "none", which gives me the error message
>
> "Fatal error:
> There is a dangling bond at at least one of the terminal ends. Fix your
> coordinate file, add a new terminal database entry (.tdb), or select the
> proper existing terminal entry."
>
> I added the flag -missing (according to Justin's advice), but does not
> help. I guess I'm not understanding what bond is dangling here, and what to
> add to the tdb file that would help?
>
> Of course, I could get most of the topology I need by avoiding selecting
> -ter 'none' but then I have to fiddle with adding back atoms.
>
> Best,
> Viveca
>
-- 
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.

[gmx-users] PCA mathematical information

[edesantis]

Dear gromacs users,

I am a PhD student in biophysics,
I am trying to preform principal component analysis on my simulations 
with the aim to understand if there are present correlated motions 
during the dynamics.


I an not expert of this kind of analysis,
I was studying different tutorials and I saw that it is common to filter 
the trajectory to show only the motion along some eigenvectors  (gmx 
anaig -filt -first -last)


I didn't understand what is the mathematical operation behind this 
operation


any of you can help me?


thank you in advance,
best regards,
Emiliano De Santis

--
Emiliano De Santis
--
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.

[gmx-users] trjcat accepts only binary formats

[András Ferenc WACHA]

Dear Gromacs Developers,

I have found that in version 2018 the trjcat program stopped supporting
.gro as an input file for the switch "-f". I have been using this
feature to concatenate several coordinate states to calculate single
point energy with gmx mdrun -rerun.

I have found a workaround to first convert the .gro files to .trr (or
.xtc) and then concatenate them, but I find that really clumsy.
Incidentally, I have also found that if I issue gmx trjconv -f
grofile.gro -o trajectory.trr (i.e. without specifying the tpr file with
-s) segfaults. If the tpr is specified, the program runs correctly and a
binary file is produced.

Do you have a better solution for this?

Thank you,

Andras Wacha

PS: The relevant output of "gmx -version" is:

GROMACS version:    2018
Precision:  single
Memory model:   64 bit
MPI library:    thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
GPU support:    disabled
SIMD instructions:  SSE4.1
FFT library:    fftw-3.3.5-sse2
RDTSCP usage:   enabled
TNG support:    enabled
Hwloc support:  hwloc-1.11.0
Tracing support:    disabled
Built on:   2018-01-14 15:27:50
Built by:   wachaandras@flambeau [CMAKE]
Build OS/arch:  Linux 4.14.13-1-ARCH x86_64
Build CPU vendor:   Intel
Build CPU brand:    Intel(R) Core(TM) i5 CPU   M 520  @ 2.40GHz
Build CPU family:   6   Model: 37   Stepping: 5
Build CPU features: aes apic clfsh cmov cx8 cx16 htt intel lahf mmx msr
nonstop_tsc pcid pclmuldq pdcm popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2
ssse3
C compiler: /usr/sbin/gcc-6 GNU 6.4.1
C compiler flags:    -msse4.1   -march=native -O2 -pipe
-fstack-protector-strong  -O3 -DNDEBUG -funroll-all-loops
-fexcess-precision=fast 
C++ compiler:   /usr/sbin/g++-6 GNU 6.4.1
C++ compiler flags:  -msse4.1   -march=native -O2 -pipe
-fstack-protector-strong -std=c++11   -O3 -DNDEBUG -funroll-all-loops
-fexcess-precision=fast 


-- 
András Ferenc Wacha, PhD
research fellow, CREDO instrument responsible

Biological Nanochemistry Research Group

Institute of Materials and Environmental Chemistry
Research Centre for Natural Sciences
Hungarian Academy of Sciences (RCNS HAS)
Magyar tudósok körútja 2.
H-1117 Budapest, Hungary
Phone: +36-1-382-6427
Web: http://bionano.ttk.mta.hu, 
CREDO SAXS instrument: http://credo.ttk.mta.hu



signature.asc
Description: OpenPGP digital signature
-- 
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.

Re: [gmx-users] gmx hbond

[Erik Marklund]

Hi Negar,

Correct, the -dist option doesn’t do what you want it to. I cannot come up with 
a recipe for how to do this, but I suspect multiple rounds of gmx select and 
gmx hbond might do the trick.

Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se

On 5 Feb 2018, at 15:49, negar habibzadeh 
> wrote:

Hi

I want to calculate *number of hydrogen bond* by *distance from center of
bilayer*.
i use gmx hbonds -dist but it doesn't give me the proper 
result.is it true?
which options should i implement to get the best result?

best regads
-negar
--
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.

-- 
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.

[gmx-users] Gibbs' free energy in MD

[Raag Saluja]

Hi!

How can I calculate Gibbs' free energy from the potential energy values
obtained from the MD simulation?

Regards,
Raag
-- 
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.

Re: [gmx-users] Rupture force definition

[Rakesh Mishra]

Thank you very much Justin.

Here it is working but having some  problem.
pull_group2_name = chain_B35  is moving in the + z direction &
pull_group4_name= chain_B26   is  moving oppositely in the -z direction
While I have given pull in +z direction for both the above group.

Note - pull_group1_name = chain_A8 and  pull_group3_name  = chain_A17 are
immobile here as well as acting as reference.


On Thu, Feb 1, 2018 at 7:16 PM, Justin Lemkul  wrote:

>
>
> On 2/1/18 7:59 AM, Rakesh Mishra wrote:
>
>> Dear Justin
>>
>> Here I am applying pull for two groups with respect to two reference group
>> as following.
>> ; Pull code
>> pull= yes
>> pull_ngroups= 4
>> pull_ncoords= 1
>> pull_group1_name= chain_A8 (reference  also immobile )
>> pull_group2_name= chain_B35   (pulling group)
>> pull_group3_name= chain_A17(reference also immobile)
>> pull_group4_name= chain_B26(pulling)
>> pull_coord1_type= umbrella  ; harmonic biasing force
>> pull_coord1_geometry= distance  ; simple distance increase
>> pull_coord1_groups  = 1 2
>> pull_coord1_dim = N N Y
>> pull_coord1_rate= 0.01  ; 0.01 nm per ps = 10 nm per 1 ns
>> pull_coord1_k   = 1000  ; kJ mol^-1 nm^-2
>> pull_coord1_start   = yes   ; define initial COM distance > 0
>>
>> In above protocol I want to make two reference group  as
>> 1-chain_A8   2- chain_A17
>> and two pull group.
>> 1- chain_B35  2- chain_B26
>>
>
> You've defined four groups but then only used two, so you only get the
> effect of one reaction coordinate.
>
> What you need to do is define the pull settings for all reaction
> coordinates simultaneously, e.g.:
>
> pull= yes
> pull_ngroups= 4
> pull_ncoords= 2
> pull_group1_name= chain_A8
> pull_group2_name= chain_B35
> pull_group3_name= chain_A17
> pull_group4_name= chain_B26
> ; definition of reaction coordinate 1, groups 1-2
> pull_coord1_type= umbrella
> pull_coord1_geometry= distance
> pull_coord1_groups  = 1 2
> pull_coord1_dim = N N Y
> pull_coord1_rate= 0.01
> pull_coord1_k   = 1000
> pull_coord1_start   = yes
> ; definition of reaction coordinate 2, groups 3-4
> pull_coord2_type= umbrella
> pull_coord2_geometry= distance
> pull_coord2_groups  = 3 4
> pull_coord2_dim = N N Y
> pull_coord2_rate= 0.01
> pull_coord2_k   = 1000
> pull_coord2_start   = yes
>
> Note that above I changed pull_ncoords to be set to 2, because you want
> two reaction coordinates. Then just specify the settings for each one,
> calling the appropriate groups by their assigned numbers.
>
> -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
>
> ==
>
> --
> 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.
>



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

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

*Phone n. +91 9473662491, +91877749632*
-- 
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.