Re: [gmx-users] GMX Error after CUDA update

[Krzysztof Kolman]

Dear Mark,

Thank you for the answer. I was afraid that this is the only possibility to
fix it.

Best,
Krzysztof

czw., 21 cze 2018 o 23:00 Mark Abraham 
napisał(a):

> Hi,
>
> Rolling distros tend to have only one version of things available, leading
> to symptoms as you describe, for which the remedy is to recompile.
>
> Mark
>
> On Thu, Jun 21, 2018 at 10:54 PM Krzysztof Kolman <
> krzysztof.kol...@gmail.com> wrote:
>
> > Dear Gromacs Users,
> >
> > After my system update (Manjaro), I can not run Gromacs anymore. I
> noticed
> > that Cuda has been update from version 9.1 to 9.2 and now I get following
> > error:
> > gmx: error while loading shared libraries: libcufft.so.9.1: cannot open
> > shared object file: No such file or directory
> >
> > Is it possible to fix it without recompiling Gromacs (I am using
> > Gromacs2018)?
> >
> > Thank you in advance for your help.
> >
> > Kind regards,
> > Krzysztof
> > --
> > Gromacs Users mailing list
> >
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> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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Re: [gmx-users] GMX Error after CUDA update

[Mark Abraham]

Hi,

Rolling distros tend to have only one version of things available, leading
to symptoms as you describe, for which the remedy is to recompile.

Mark

On Thu, Jun 21, 2018 at 10:54 PM Krzysztof Kolman <
krzysztof.kol...@gmail.com> wrote:

> Dear Gromacs Users,
>
> After my system update (Manjaro), I can not run Gromacs anymore. I noticed
> that Cuda has been update from version 9.1 to 9.2 and now I get following
> error:
> gmx: error while loading shared libraries: libcufft.so.9.1: cannot open
> shared object file: No such file or directory
>
> Is it possible to fix it without recompiling Gromacs (I am using
> Gromacs2018)?
>
> Thank you in advance for your help.
>
> Kind regards,
> Krzysztof
> --
> Gromacs Users mailing list
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> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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[gmx-users] GMX Error after CUDA update

[Krzysztof Kolman]

Dear Gromacs Users,

After my system update (Manjaro), I can not run Gromacs anymore. I noticed
that Cuda has been update from version 9.1 to 9.2 and now I get following
error:
gmx: error while loading shared libraries: libcufft.so.9.1: cannot open
shared object file: No such file or directory

Is it possible to fix it without recompiling Gromacs (I am using
Gromacs2018)?

Thank you in advance for your help.

Kind regards,
Krzysztof
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Re: [gmx-users] Magnetic field in GROMACS

[حبيبة علي]

Dear Alex,

Thanks for your words. Yes, we have going on research and we look to the
future. But we are suffering from the lack of resources.

We did some work on electric field code but we could not call the velocity
of each particle to do the cross product with the magnetic field and also
our coding skills are horrible ;).

Thanks


On Thu, Jun 21, 2018 at 3:47 AM, Alex  wrote:

> I would at least first try to hardcode a test Lorentz force for e.g. a
> given constant magnetic field to see what happens and whether you can
> observe anything fun.
>
> On an unrelated note, I just want to say that it is great to see that
> there is scientific research going on in Iraq after years of war and
> destruction. Hats off to you and very best of luck!
>
> Alex
>
>
>
> On 6/21/2018 2:22 AM, حبيبة علي wrote:
>
>> I thought you are a developer ;)
>> I think updating electric field file is not a problem but the
>> complicated thing is what are the other files that related to it. Such as
>> how to implement it in mdp files which I think need to update different
>> files. If there are any analyzing commands need updating, etc
>> I  will keep trying
>> Thanks
>>
>>
>> On Thu, Jun 21, 2018 at 2:24 AM, Alex  wrote:
>>
>> Nah, I'm just a user. ;)
>>>
>>> What David and I were discussing is not a beginner's task (and I can't
>>> see
>>> a large number of users for that otherwise awesome functionality), but if
>>> you'd like to code the simple vector product, I am pretty sure there will
>>> be those who could direct you to the right files.
>>>
>>> Alex
>>>
>>>
>>>
>>> On 6/21/2018 1:08 AM, حبيبة علي wrote:
>>>
>>> Dear David and Alex,

 Thanks for the replies. I'm happy that you will consider it. You are the
 developers and it is clear for you which file should be updated;

 Dear Ali,
 My coding skills are very bad and I have no idea which file I need to
 look
 at.

 Best

 On Wed, Jun 20, 2018 at 12:02 PM, Ali Ahmed 
 wrote:

 Hello,

> I looked for that before and I tried updating the electric field code
> as
> both of them are related to Lorentz force. Unfortunately, I failed
> because
> there are different codes need to be updated.
> It would be amazing if the developers participate in this code.
> Thanks
> Ali
>
> On Wed, Jun 20, 2018 at 3:28 AM, David van der Spoel <
> sp...@xray.bmc.uu.se
> wrote:
>
> Den 2018-06-20 kl. 10:20, skrev Alex:
>
>> David,
>>
>>> I can think of many realistic cases when looking at the effects of
>>> magnetic fields in MD would be of interest, just not in what Gromacs
>>> is
>>> normally used for.
>>>
>>> It's just a completely different animal in terms of what causes those
>>> effects and Lorentz force applied to point charges would likely be a
>>>
>>> very
>> bad approximation. But in general, an implementation of
>> self-consistent
>>
>>> MD+FDTD (i.e. MD + Maxwell's eqns) would be pretty amazing.
>>>
>>> Feel free to open a redmine issue to discuss it there.
>>>
>> We have an implementation of electric fields that can be used as a
>> template.
>>
>>
>> Alex
>>
>>>
>>>
>>> Magnetic fields are typically very weak such that they are negligable
>>> in
>>>
>> realistic cases. This is why nobody bothered to implement it.
>>
>>>
 --

>>> 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.
>> http://www.icm.uu.se
>> --
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>>
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Re: [gmx-users] how to improve computing?

[Владимир Богданов]

Szilárd, I attached .log file. Can does it mean I can use two graphic cards with this processor to improve calculation? Best regards,Vlad 14.06.2018, 18:14, "Szilárd Páll" :Vlad,Please share your log file(s), it's easier to be concrete about a concrete case.mdrun will by default attempt to use all resources available, unlessthere are some hard limitations that prevent this (e.g. very smallnumber of atoms can't be decomposed) or there is a reason to believethat doing so will be detrimental to the performance. Your log filewill contain all/most of such override information.You can always select manually to use all threads by specifying e.g.-ntomp 16 to use 16 threads per rank/GPU.Cheers,--SzilárdOn Thu, Jun 14, 2018 at 4:38 AM, Владимир Богданов wrote: Hey everyone! Could help me somebody, please. I have PC with 8 cores, 16 logical cores and 1 compatible GPU, but gromacs calculates just with 1GPU, 1MPI thread and 8 OpenMP threads. Would it possible for me to use all of 16 logical cores? i7-7820X Nvidia Titan Xp gromacs 2018 CUDA=on Ubuntu 16.04 -- Thanks, Vlad -- 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 visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.  -- C уважением, Владимир А. Богданов Log file opened on Wed Jun 20 00:21:32 2018
Host: vlad  pid: 2520  rank ID: 0  number of ranks:  1
   :-) GROMACS - gmx mdrun, 2018 (-:

GROMACS is written by:
 Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar Bjelkmar   
 Aldert van Buuren   Rudi van Drunen Anton FeenstraGerrit Groenhof  
 Christoph Junghans   Anca HamuraruVincent Hindriksen Dimitrios Karkoulis
Peter KassonJiri Kraus  Carsten Kutzner  Per Larsson
  Justin A. LemkulViveca LindahlMagnus Lundborg   Pieter Meulenhoff 
   Erik Marklund  Teemu Murtola   Szilard Pall   Sander Pronk   
   Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers  
   Peter TielemanTeemu Virolainen  Christian WennbergMaarten Wolf   
   and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2017, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
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 2018
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Working dir:  /home/vlad/study/epidermin/ep_run/run_dp/extra
Command line:
  gmx mdrun -s md.tpr -deffnm MD

GROMACS version:2018
Precision:  single
Memory model:   64 bit
MPI library:thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
GPU support:CUDA
SIMD instructions:  AVX_512
FFT library:fftw-3.3.5-fma-sse2-avx-avx2-avx2_128-avx512
RDTSCP usage:   enabled
TNG support:enabled
Hwloc support:  disabled
Tracing support:disabled
Built on:   2018-06-13 00:12:23
Built by:   vlad@vlad [CMAKE]
Build OS/arch:  Linux 4.13.0-45-generic x86_64
Build CPU vendor:   Intel
Build CPU brand:Intel(R) Core(TM) i7-7820X CPU @ 3.60GHz
Build CPU family:   6   Model: 85   Stepping: 4
Build CPU features: aes apic avx avx2 avx512f avx512cd avx512bw avx512vl clfsh 
cmov cx8 cx16 f16c fma hle htt intel lahf mmx msr nonstop_tsc pcid pclmuldq 
pdcm pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt 
x2apic
C compiler: /usr/bin/cc GNU 5.4.0
C compiler flags:-mavx512f -mfma -O3 -DNDEBUG -funroll-all-loops 
-fexcess-precision=fast  
C++ compiler:   /usr/bin/c++ GNU 5.4.0
C++ compiler flags:  -mavx512f -mfma-std=c++11   -O3 -DNDEBUG 
-funroll-all-loops -fexcess-precision=fast  
CUDA compiler:  /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler 
driver;Copyright (c) 2005-2018 NVIDIA Corporation;Built on 
Wed_Apr_11_23:16:29_CDT_2018;Cuda compilation tools, release 9.2, V9.2.88
CUDA compiler 

Re: [gmx-users] GTX 960 vs Tesla K40

[Szilárd Páll]

On Mon, Jun 18, 2018 at 11:35 PM Alex  wrote:

> Persistence is enabled so I don't have to overclock again.


Sure, makes sense. Note that strictly speaking this is not an "overclock",
but a manual "boost clock" (to use terminology CPU vendors use). Consumer
GPUs automatically scale their clock speeds above their nominal/base clock
(just as CPUs do), but Tesla GPUs don't do that but rather give the option
on the user (or put the burden if we want to look at it differently).


> To be honest, I
> am still not entirely comfortable with the notion of ranks, after reading
> the acceleration document a bunch of times.


Feel free to ask if you need clarification.
Briefly: ranks are the execution units, typically MPI processes, that tasks
get assigned to when decomposing work across multiple compute units (nodes,
processors). In general, data or tasks can be decomposed (also called
data-/task-parallelization), and GROMACS does employ both, the former for
the spatial domain decomposition, the latter for offloading PME work to a
subset of the ranks.


> Parts of log file below and I
> will obviously appreciate suggestions/clarifications:
>

In the future, please share the full log by uploading it somewhere.


> Command line:
>   gmx mdrun -nt 4 -ntmpi 2 -npme 1 -pme gpu -nb gpu -s run_unstretch.tpr -o
> traj_unstretch.trr -g md.log -c unstretched.gro
>

As noted before, I doubt that you benefit from using a separate PME rank
with a single GPU.

I suggest that instead you simply run:
gmx mdrun -ntmpi 1 -pme gpu -nb gpu
optionally, you can pass -ntomp 4, but that's the default so it's not
needed.


>
> GROMACS version:2018
> Precision:  single
> Memory model:   64 bit
> MPI library:thread_mpi
> OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
> GPU support:CUDA
> SIMD instructions:  SSE4.1
> FFT library:fftw-3.3.5-sse2
> RDTSCP usage:   enabled
> TNG support:enabled
> Hwloc support:  disabled
> Tracing support:disabled
> Built on:   2018-02-13 19:43:29
> Built by:   smolyan@MINTbox [CMAKE]
> Build OS/arch:  Linux 4.4.0-112-generic x86_64
> Build CPU vendor:   Intel
> Build CPU brand:Intel(R) Xeon(R) CPU   W3530  @ 2.80GHz
> Build CPU family:   6   Model: 26   Stepping: 5
> Build CPU features: apic clfsh cmov cx8 cx16 htt intel lahf mmx msr
> nonstop_tsc pdcm popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3
> C compiler: /usr/bin/cc GNU 5.4.0
> C compiler flags:-msse4.1 -O3 -DNDEBUG -funroll-all-loops
> -fexcess-precision=fast
> C++ compiler:   /usr/bin/c++ GNU 5.4.0
> C++ compiler flags:  -msse4.1-std=c++11   -O3 -DNDEBUG
> -funroll-all-loops -fexcess-precision=fast
> CUDA compiler:  /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler
> driver;Copyright (c) 2005-2017 NVIDIA Corporation;Built on
> Fri_Nov__3_21:07:56_CDT_2017;Cuda compilation tools, release 9.1, V9.1.85
> CUDA compiler
>
> flags:-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_70,code=sm_70;-gencode;arch=compute_70,code=compute_70;-use_fast_math;-D_FORCE_INLINES;;
>
> ;-msse4.1;-std=c++11;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast;
> CUDA driver:9.10
> CUDA runtime:   9.10
>
>
> Running on 1 node with total 4 cores, 4 logical cores, 1 compatible GPU
> Hardware detected:
>   CPU info:
> Vendor: Intel
> Brand:  Intel(R) Xeon(R) CPU   W3530  @ 2.80GHz
> Family: 6   Model: 26   Stepping: 5
> Features: apic clfsh cmov cx8 cx16 htt intel lahf mmx msr nonstop_tsc
> pdcm popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3
>   Hardware topology: Basic
> Sockets, cores, and logical processors:
>   Socket  0: [   0]
>   Socket  1: [   1]
>   Socket  2: [   2]
>   Socket  3: [   3]
>   GPU info:
> Number of GPUs detected: 1
> #0: NVIDIA Tesla K40c, compute cap.: 3.5, ECC:  no, stat: compatible
>
> 
>
> M E G A - F L O P S   A C C O U N T I N G
>
>  NB=Group-cutoff nonbonded kernelsNxN=N-by-N cluster Verlet kernels
>  RF=Reaction-Field  VdW=Van der Waals  QSTab=quadratic-spline table
>  W3=SPC/TIP3p  W4=TIP4p (single or pairs)
>  V=Potential and force  V=Potential only  F=Force only
>
>  Computing:   M-Number M-Flops  % Flops
>
> -
>  Pair Search distance check  547029.956656 4923269.610 0.0
>  NxN Ewald Elec. + LJ [F] 485658021.416832 32053429413.51198.0
>  NxN Ewald Elec. + LJ [V] 4905656.839680   524905281.846 1.6
>  1,4 nonbonded interactions  140625.00562512656250.506 0.0
>  Reset In Box  4599.00   13797.000 0.0
>  

Re: [gmx-users] Dihedrals/Impropers

[Justin Lemkul]

On 6/21/18 10:22 AM, Salman Zarrini wrote:

Dear all,

I wonder if it is necessary to list all the Dihedrals/Impropers of the
molecule in a MD simulation? If not so, what kind of Dihedrals we don't
need to list?


The topology needs to contain every interaction that's relevant. Nothing 
is implicit or assumed. Most existing functional forms have dihedrals on 
every torsion, although sometimes they have force constants set to zero 
so that topological integrity can easily be checked. The use of 
impropers depends on the force field and its convention.


-Justin

--
==

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

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

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

==

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[gmx-users] Dihedrals/Impropers

[Salman Zarrini]

Dear all,

I wonder if it is necessary to list all the Dihedrals/Impropers of the
molecule in a MD simulation? If not so, what kind of Dihedrals we don't
need to list?

Thank you.

Regards,
Salman
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Re: [gmx-users] Deuterium atoms

[Smith, Micholas D.]

Typically, deuterium is treated with the same parameters as H, but with double 
the mass. Most papers don't even bother with the re-parameterization, using the 
argument that the bond-lengths will not change substantially. Instead the 
authors focus on how the dynamics are slowed. 

If you really want to use deuterium properly you should consider 
re-parameterizing, but it really boils down to what phenomena you are most 
interested in looking at? Which begs the question, why are you using D instead 
of H? Are you trying to match an experiment that had deuterurated samples?

As an aside, If this is extremely low-temp or related to proton tunneling then 
you may also need to consider not doing traditional MD, but instead 
Ring-Polymer MD (i.e. Path Integral Molecular Dynamics), because the BO 
approximation may not applicable. But then you can't use gromacs for that...

===
Micholas Dean Smith, PhD. MRSC
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Justin Lemkul 

Sent: Thursday, June 21, 2018 9:09 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Deuterium atoms

On 6/21/18 9:05 AM, Hermann, Johannes wrote:
> Hello Justin,
>
> okay that is beyond my expertise. Do you know / think if there will be
> a force field in the future where deuterium is present?
>

There are tons of published studies that have done MD with deuterium. I
suggest you start there.

-Justin

> All the best
>
> Johannes
>
>
> On 21.06.2018 15:01, Justin Lemkul wrote:
>>
>>
>> On 6/21/18 8:53 AM, Hermann, Johannes wrote:
>>> Hello Justin,
>>>
>>> thank you for your answer. So the only way to simulate with
>>> deuterium atoms would be a parametrization of the force field, in
>>> particular the bonded force constant?
>>>
>>
>> At minimum. All parameters are connected, so angles and dihedrals may
>> be affected by different vibrational frequencies.
>>
>> -Justin
>>
>>> Thank you in advance!
>>>
>>> All the best
>>>
>>> Johannes
>>>
>>>
>>> On 21.06.2018 14:16, Justin Lemkul wrote:


 On 6/21/18 3:47 AM, Hermann, Johannes wrote:
> Thanks Vytautas, might solve it! And additionally change the mass
> in the force field.
>
>

 Increasing the mass will also change the vibrational frequency of
 any bonds involved, requiring a reparametrization of the bonded
 force constant. If you're using constraints, this does not matter,
 but then I sort of wonder why you're bothering to replace H with D
 and expect to see any kind of difference.

 -Justin

> On 21.06.2018 09:24, Vytautas Rakeviius wrote:
>> 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
>>
>

>>>
>>
>

--
==

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] Deuterium atoms

[Justin Lemkul]

On 6/21/18 9:05 AM, Hermann, Johannes wrote:

Hello Justin,

okay that is beyond my expertise. Do you know / think if there will be 
a force field in the future where deuterium is present?




There are tons of published studies that have done MD with deuterium. I 
suggest you start there.


-Justin


All the best

Johannes


On 21.06.2018 15:01, Justin Lemkul wrote:



On 6/21/18 8:53 AM, Hermann, Johannes wrote:

Hello Justin,

thank you for your answer. So the only way to simulate with 
deuterium atoms would be a parametrization of the force field, in 
particular the bonded force constant?




At minimum. All parameters are connected, so angles and dihedrals may 
be affected by different vibrational frequencies.


-Justin


Thank you in advance!

All the best

Johannes


On 21.06.2018 14:16, Justin Lemkul wrote:



On 6/21/18 3:47 AM, Hermann, Johannes wrote:
Thanks Vytautas, might solve it! And additionally change the mass 
in the force field.





Increasing the mass will also change the vibrational frequency of 
any bonds involved, requiring a reparametrization of the bonded 
force constant. If you're using constraints, this does not matter, 
but then I sort of wonder why you're bothering to replace H with D 
and expect to see any kind of difference.


-Justin


On 21.06.2018 09:24, Vytautas Rakeviius wrote:

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













--
==

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] Deuterium atoms

[Hermann, Johannes]

Hello Justin,

okay that is beyond my expertise. Do you know / think if there will be a 
force field in the future where deuterium is present?


All the best

Johannes


On 21.06.2018 15:01, Justin Lemkul wrote:



On 6/21/18 8:53 AM, Hermann, Johannes wrote:

Hello Justin,

thank you for your answer. So the only way to simulate with deuterium 
atoms would be a parametrization of the force field, in particular 
the bonded force constant?




At minimum. All parameters are connected, so angles and dihedrals may 
be affected by different vibrational frequencies.


-Justin


Thank you in advance!

All the best

Johannes


On 21.06.2018 14:16, Justin Lemkul wrote:



On 6/21/18 3:47 AM, Hermann, Johannes wrote:
Thanks Vytautas, might solve it! And additionally change the mass 
in the force field.





Increasing the mass will also change the vibrational frequency of 
any bonds involved, requiring a reparametrization of the bonded 
force constant. If you're using constraints, this does not matter, 
but then I sort of wonder why you're bothering to replace H with D 
and expect to see any kind of difference.


-Justin


On 21.06.2018 09:24, Vytautas Rakeviius wrote:

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] Deuterium atoms

[Justin Lemkul]

On 6/21/18 8:53 AM, Hermann, Johannes wrote:

Hello Justin,

thank you for your answer. So the only way to simulate with deuterium 
atoms would be a parametrization of the force field, in particular the 
bonded force constant?




At minimum. All parameters are connected, so angles and dihedrals may be 
affected by different vibrational frequencies.


-Justin


Thank you in advance!

All the best

Johannes


On 21.06.2018 14:16, Justin Lemkul wrote:



On 6/21/18 3:47 AM, Hermann, Johannes wrote:
Thanks Vytautas, might solve it! And additionally change the mass in 
the force field.





Increasing the mass will also change the vibrational frequency of any 
bonds involved, requiring a reparametrization of the bonded force 
constant. If you're using constraints, this does not matter, but then 
I sort of wonder why you're bothering to replace H with D and expect 
to see any kind of difference.


-Justin


On 21.06.2018 09:24, Vytautas Rakeviius wrote:

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









--
==

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] Deuterium atoms

[Hermann, Johannes]

Hello Justin,

thank you for your answer. So the only way to simulate with deuterium 
atoms would be a parametrization of the force field, in particular the 
bonded force constant?


Thank you in advance!

All the best

Johannes


On 21.06.2018 14:16, Justin Lemkul wrote:



On 6/21/18 3:47 AM, Hermann, Johannes wrote:
Thanks Vytautas, might solve it! And additionally change the mass in 
the force field.





Increasing the mass will also change the vibrational frequency of any 
bonds involved, requiring a reparametrization of the bonded force 
constant. If you're using constraints, this does not matter, but then 
I sort of wonder why you're bothering to replace H with D and expect 
to see any kind of difference.


-Justin


On 21.06.2018 09:24, Vytautas Rakeviius wrote:

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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[gmx-users] Implicit solvent

[Chhaya Singh]

:

> 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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[gmx-users] fatal error with mpi

[Stefano Guglielmo]

Dear users,

I have installed gromacs with MPI instead of its native tMPI and I am
encountering the following error:
"Fatal error:
4 particles communicated to PME rank 5 are more than 2/3 times the cut-off
out
of the domain decomposition cell of their charge group in dimension y.
This usually means that your system is not well equilibrated."

I am using 8 MPI ranks with 4 omp threads per rank (it was the
configuration used on the same machine by tMPI), but I also tried 4 ranks
with 8 threads, but it did not solve the problem.

I don't think this is an issue related to my system because the same system
run with the native tMPI works properly (it has already been termalized and
gradually equilibrated); neverthless I tried to reduce dt and temperature
but without any benefit. Does anybody have any suggestions?

Thanks in advance
Stefano

-- 
Stefano GUGLIELMO PhD
Assistant Professor of Medicinal Chemistry
Department of Drug Science and Technology
Via P. Giuria 9
10125 Turin, ITALY
ph. +39 (0)11 6707178
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Re: [gmx-users] No line with moleculetype 'SOL' found the [ molecules ] section

[Gonzalez Fernandez, Cristina]

Dear Justin,

Thank you for your suggestion. I have solved the problem!

C.

-Mensaje original-
De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] En nombre de Justin 
Lemkul
Enviado el: jueves, 21 de junio de 2018 1:11
Para: gmx-us...@gromacs.org
Asunto: Re: [gmx-users] No line with moleculetype 'SOL' found the [ molecules ] 
section



On 6/19/18 3:59 AM, Gonzalez Fernandez, Cristina wrote:
> Dear Gromacs users,
> I am trying adding Na ions:
> genion -s ions.tpr -o 1lipidA_solv.g96 -p lipidA_gromacsBien.top 
> -pname NA -np 2
>
> But I get this error:
> Fatal error:
> No line with moleculetype 'SOL' found the [ molecules ] section of file 
> 'lipidA_gromacsBien.top'
>
> I have check the .top file and I have defined "SOL" in the [ moleculetype ] 
> section before [ molecules ] section:
> [ moleculetype ]
> ; molname   nrexcl
> SOL 3
> [ molecules ]
> ; Compound#mols
> MOL_1 1
> SOL4049
> Also, I have checked the Gromacs manual and other Gromacs users discussion. 
> However, I don´t know how to solve this error, because I think SOL is well 
> defined in the .top file.
> I attach the .top file
> Could anyone help me?

Likely you've got a Windows-style line ending from using a non-plain text 
editor. Use dos2unix and make sure to only edit files in proper editors like 
vim, emacs, etc.

-Justin

--
==

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

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

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

==

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Re: [gmx-users] opnempi

[Stefano Guglielmo]

Thanks,
I did it

2018-06-21 1:08 GMT+02:00 Benson Muite :

> Hi,
>
> Might try using ccmake to get user interface and check variables are setup
> correctly.
>
> Regards,
> Benson
>
> On 06/21/2018 02:03 AM, Stefano Guglielmo wrote:
>
>> Dear gromacs users,
>>
>> I am trying to compile gromacs 2016.5 with openmpi compilers installed on
>> my machine; here is the configuration command:
>>
>> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=on
>> -DGMX_MPI=on -DMPI_C_COMPILER=/usr/lib64/openmpi/bin/mpicc
>> -DMPI_CXX_COMPILER=/usr/lib64/openmpi/bin/mpicxx
>>
>> compilation and installation end up correctly, but when trying to run
>> mdrun, gromacs still uses its own tMPI; how can I avoid tMPI and "force"
>> to
>> MPI?
>>
>> Thanks in advance
>> Stefano
>>
>> --
> Gromacs Users mailing list
>
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> /Mailing_Lists/GMX-Users_List before posting!
>
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> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
Stefano GUGLIELMO PhD
Assistant Professor of Medicinal Chemistry
Department of Drug Science and Technology
Via P. Giuria 9
10125 Turin, ITALY
ph. +39 (0)11 6707178
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Re: [gmx-users] Continuation of the gromacs job using gmx convert-tpr

[Justin Lemkul]

On 6/21/18 2:35 AM, Own 12121325 wrote:

and without append flag it will produce an output in the separate file,
won't it?


No, because appending is the default behavior. Specifying -append just 
invokes what mdrun does on its own. If you want a separate file, add 
-noappend to your mdrun command.


-Justin


gmx convert-tpr -s init.tpr -o next.tpr -extend 50
gmx mdrun -s next.tpr -cpi the_last_chekpoint.cpt

2018-06-21 1:12 GMT+02:00 Justin Lemkul :



On 6/19/18 4:45 AM, Own 12121325 wrote:


Hello Justin,

could you specify please a bit more. Following your method, if the
simulation has been terminated by crash without producing gro file so to
re-initiate it I only need one command:

gmx mdrun -s initial.tpr -cpi the_last_chekpoint.cpt -append

where the last_checkpoint should be something like initial.cpt or
initial_prev.cpt


Right.

but In case if my simulation has been finished correctly e.g. for 50 ns and

I now need to extend it for another 50 ns,  should I do the following
trick
with 2 GMX programs:

gmx convert-tpr -s init.tpr -o next.tpr -extend 50
gmx mdrun -s next.tpr -cpi the_last_chekpoint.cpt -append

it will produce the second part of the trajectory as the new file
(next.trr) or merge together the first and the second part ?


You're specifying -append, so the output will be concatenated by mdrun.
That's also been default behavior for as long as I can remember, too :)

-Justin

--
==

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

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

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

==

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--
==

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] Deuterium atoms

[Justin Lemkul]

On 6/21/18 3:47 AM, Hermann, Johannes wrote:
Thanks Vytautas, might solve it! And additionally change the mass in 
the force field.





Increasing the mass will also change the vibrational frequency of any 
bonds involved, requiring a reparametrization of the bonded force 
constant. If you're using constraints, this does not matter, but then I 
sort of wonder why you're bothering to replace H with D and expect to 
see any kind of difference.


-Justin


On 21.06.2018 09:24, Vytautas Rakeviius wrote:

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





--
==

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] FFTW compiler error: no such instruction

[Mateusz Bieniek]

A quick update. FFTW is supposed to create fat binaries and ignore the AVX
that it cannot use. Regardless, this did not happen the right way. I've
modified the src/contrib/fftw/CMakeFiles/fftwBuild.dir/build.make and
removed the --enable- "512avx" and other terms and this removed the issue.

Thanks, Mat

On Thu, Jun 21, 2018 at 11:04 AM Mateusz Bieniek 
wrote:

> Dear Gromacsers,
>
> After compiling gromacs successfully with SSE4.1 it suggested AVX_256
> instead. With AVX_256 the compilation is interrupted with the FFTW error
> below. In this case I am in need of more CPU power due to the multiple GPUs
> installed.
>
> --
> libtool: compile:  /opt/apps/compilers/gcc/5.3.0/bin/gcc -DHAVE_CONFIG_H
> -I.
> -I/.../gromacs-2018.2/buildavx/src/contrib/fftw/fftwBuild-prefix/src/fftwBuild/dft/simd/avx2-128
> -I../../.. -I
> /.../gromacs-2018.2/buildavx/src/contrib/fftw/fftwBuild-prefix/src/fftwBuild
> -march=core-avx2 -mfma -O3 -fomit-frame-pointer -mtune=native
> -malign-double -fstrict-aliasing -fno-schedule-insns -MT n2sv_32.lo -MD -MP
> -MF .deps/n2sv_32.Tpo -c
> /gromacs-2018.2/buildavx/src/contrib/fftw/fftwBuild-prefix/src/fftwBuild/dft/simd/avx2-128/n2sv_32.c
> -fPIC -DPIC -o n2sv_32.o
> /tmp/cczju8Es.s: Assembler messages:
> /tmp/cczju8Es.s:33: Error: no such instruction: `shlx %rbx,56(%rsp),%rbx'
> make[8]: *** [n2sv_4.lo] Error 1
> make[8]: *** Waiting for unfinished jobs
> /tmp/ccsZIbpx.s: Assembler messages:
> /tmp/ccsZIbpx.s:35: Error: no such instruction: `shlx %rbx,64(%rsp),%rbp'
> make[8]: *** [n2sv_8.lo] Error 1
> /tmp/ccdxksFN.s: Assembler messages:
> /tmp/ccdxksFN.s:50: Error: no such instruction: `shlx %rbx,400(%rsp),%rbx'
> make[8]: *** [n2sv_16.lo] Error 1
> /tmp/ccTdLLjQ.s: Assembler messages:
> /tmp/ccTdLLjQ.s:68: Error: no such instruction: `shlx %rbx,1168(%rsp),%rbx'
>
> Any suggestions are welcome.
>
> Thanks, Mateusz
>
>
> Linux: Scientific Linux release 6.6 (Carbon)
> gcc 5.3.0
>
>
>
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[gmx-users] FFTW compiler error: no such instruction

[Mateusz Bieniek]

Dear Gromacsers,

After compiling gromacs successfully with SSE4.1 it suggested AVX_256
instead. With AVX_256 the compilation is interrupted with the FFTW error
below. In this case I am in need of more CPU power due to the multiple GPUs
installed.

--
libtool: compile:  /opt/apps/compilers/gcc/5.3.0/bin/gcc -DHAVE_CONFIG_H
-I.
-I/.../gromacs-2018.2/buildavx/src/contrib/fftw/fftwBuild-prefix/src/fftwBuild/dft/simd/avx2-128
-I../../.. -I
/.../gromacs-2018.2/buildavx/src/contrib/fftw/fftwBuild-prefix/src/fftwBuild
-march=core-avx2 -mfma -O3 -fomit-frame-pointer -mtune=native
-malign-double -fstrict-aliasing -fno-schedule-insns -MT n2sv_32.lo -MD -MP
-MF .deps/n2sv_32.Tpo -c
/gromacs-2018.2/buildavx/src/contrib/fftw/fftwBuild-prefix/src/fftwBuild/dft/simd/avx2-128/n2sv_32.c
-fPIC -DPIC -o n2sv_32.o
/tmp/cczju8Es.s: Assembler messages:
/tmp/cczju8Es.s:33: Error: no such instruction: `shlx %rbx,56(%rsp),%rbx'
make[8]: *** [n2sv_4.lo] Error 1
make[8]: *** Waiting for unfinished jobs
/tmp/ccsZIbpx.s: Assembler messages:
/tmp/ccsZIbpx.s:35: Error: no such instruction: `shlx %rbx,64(%rsp),%rbp'
make[8]: *** [n2sv_8.lo] Error 1
/tmp/ccdxksFN.s: Assembler messages:
/tmp/ccdxksFN.s:50: Error: no such instruction: `shlx %rbx,400(%rsp),%rbx'
make[8]: *** [n2sv_16.lo] Error 1
/tmp/ccTdLLjQ.s: Assembler messages:
/tmp/ccTdLLjQ.s:68: Error: no such instruction: `shlx %rbx,1168(%rsp),%rbx'

Any suggestions are welcome.

Thanks, Mateusz


Linux: Scientific Linux release 6.6 (Carbon)
gcc 5.3.0
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Re: [gmx-users] Magnetic field in GROMACS

[Alex]

I would at least first try to hardcode a test Lorentz force for e.g. a 
given constant magnetic field to see what happens and whether you can 
observe anything fun.


On an unrelated note, I just want to say that it is great to see that 
there is scientific research going on in Iraq after years of war and 
destruction. Hats off to you and very best of luck!


Alex


On 6/21/2018 2:22 AM, حبيبة علي wrote:

I thought you are a developer ;)
I think updating electric field file is not a problem but the
complicated thing is what are the other files that related to it. Such as
how to implement it in mdp files which I think need to update different
files. If there are any analyzing commands need updating, etc
I  will keep trying
Thanks


On Thu, Jun 21, 2018 at 2:24 AM, Alex  wrote:


Nah, I'm just a user. ;)

What David and I were discussing is not a beginner's task (and I can't see
a large number of users for that otherwise awesome functionality), but if
you'd like to code the simple vector product, I am pretty sure there will
be those who could direct you to the right files.

Alex



On 6/21/2018 1:08 AM, حبيبة علي wrote:


Dear David and Alex,

Thanks for the replies. I'm happy that you will consider it. You are the
developers and it is clear for you which file should be updated;

Dear Ali,
My coding skills are very bad and I have no idea which file I need to look
at.

Best

On Wed, Jun 20, 2018 at 12:02 PM, Ali Ahmed  wrote:

Hello,

I looked for that before and I tried updating the electric field code as
both of them are related to Lorentz force. Unfortunately, I failed
because
there are different codes need to be updated.
It would be amazing if the developers participate in this code.
Thanks
Ali

On Wed, Jun 20, 2018 at 3:28 AM, David van der Spoel <
sp...@xray.bmc.uu.se
wrote:

Den 2018-06-20 kl. 10:20, skrev Alex:

David,

I can think of many realistic cases when looking at the effects of
magnetic fields in MD would be of interest, just not in what Gromacs is
normally used for.

It's just a completely different animal in terms of what causes those
effects and Lorentz force applied to point charges would likely be a


very
bad approximation. But in general, an implementation of self-consistent

MD+FDTD (i.e. MD + Maxwell's eqns) would be pretty amazing.

Feel free to open a redmine issue to discuss it there.

We have an implementation of electric fields that can be used as a
template.


Alex



Magnetic fields are typically very weak such that they are negligable
in

realistic cases. This is why nobody bothered to implement it.


--

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Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
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Re: [gmx-users] Magnetic field in GROMACS

[حبيبة علي]

I thought you are a developer ;)
I think updating electric field file is not a problem but the
complicated thing is what are the other files that related to it. Such as
how to implement it in mdp files which I think need to update different
files. If there are any analyzing commands need updating, etc
I  will keep trying
Thanks


On Thu, Jun 21, 2018 at 2:24 AM, Alex  wrote:

> Nah, I'm just a user. ;)
>
> What David and I were discussing is not a beginner's task (and I can't see
> a large number of users for that otherwise awesome functionality), but if
> you'd like to code the simple vector product, I am pretty sure there will
> be those who could direct you to the right files.
>
> Alex
>
>
>
> On 6/21/2018 1:08 AM, حبيبة علي wrote:
>
>> Dear David and Alex,
>>
>> Thanks for the replies. I'm happy that you will consider it. You are the
>> developers and it is clear for you which file should be updated;
>>
>> Dear Ali,
>> My coding skills are very bad and I have no idea which file I need to look
>> at.
>>
>> Best
>>
>> On Wed, Jun 20, 2018 at 12:02 PM, Ali Ahmed  wrote:
>>
>> Hello,
>>> I looked for that before and I tried updating the electric field code as
>>> both of them are related to Lorentz force. Unfortunately, I failed
>>> because
>>> there are different codes need to be updated.
>>> It would be amazing if the developers participate in this code.
>>> Thanks
>>> Ali
>>>
>>> On Wed, Jun 20, 2018 at 3:28 AM, David van der Spoel <
>>> sp...@xray.bmc.uu.se
>>> wrote:
>>>
>>> Den 2018-06-20 kl. 10:20, skrev Alex:

 David,
>
> I can think of many realistic cases when looking at the effects of
> magnetic fields in MD would be of interest, just not in what Gromacs is
> normally used for.
>
> It's just a completely different animal in terms of what causes those
> effects and Lorentz force applied to point charges would likely be a
>
 very
>>>
 bad approximation. But in general, an implementation of self-consistent
> MD+FDTD (i.e. MD + Maxwell's eqns) would be pretty amazing.
>
> Feel free to open a redmine issue to discuss it there.
 We have an implementation of electric fields that can be used as a
 template.


 Alex
>
>
>
> Magnetic fields are typically very weak such that they are negligable
>>
> in
>>>
 realistic cases. This is why nobody bothered to implement it.
>>
>>
>> --
 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.
 http://www.icm.uu.se
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Department of Chemistry,
University of Mosul-Iraq
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Re: [gmx-users] S-nitrosoylated proteins

[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

[Hermann, Johannes]

Thanks Vytautas, might solve it! And additionally change the mass in the 
force field.



On 21.06.2018 09:24, Vytautas Rakeviius wrote:

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] Deuterium atoms

[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] Magnetic field in GROMACS

[Alex]

Nah, I'm just a user. ;)

What David and I were discussing is not a beginner's task (and I can't 
see a large number of users for that otherwise awesome functionality), 
but if you'd like to code the simple vector product, I am pretty sure 
there will be those who could direct you to the right files.


Alex


On 6/21/2018 1:08 AM, حبيبة علي wrote:

Dear David and Alex,

Thanks for the replies. I'm happy that you will consider it. You are the
developers and it is clear for you which file should be updated;

Dear Ali,
My coding skills are very bad and I have no idea which file I need to look
at.

Best

On Wed, Jun 20, 2018 at 12:02 PM, Ali Ahmed  wrote:


Hello,
I looked for that before and I tried updating the electric field code as
both of them are related to Lorentz force. Unfortunately, I failed because
there are different codes need to be updated.
It would be amazing if the developers participate in this code.
Thanks
Ali

On Wed, Jun 20, 2018 at 3:28 AM, David van der Spoel 
Den 2018-06-20 kl. 10:20, skrev Alex:


David,

I can think of many realistic cases when looking at the effects of
magnetic fields in MD would be of interest, just not in what Gromacs is
normally used for.

It's just a completely different animal in terms of what causes those
effects and Lorentz force applied to point charges would likely be a

very

bad approximation. But in general, an implementation of self-consistent
MD+FDTD (i.e. MD + Maxwell's eqns) would be pretty amazing.


Feel free to open a redmine issue to discuss it there.
We have an implementation of electric fields that can be used as a
template.



Alex




Magnetic fields are typically very weak such that they are negligable

in

realistic cases. This is why nobody bothered to implement it.



--
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.
http://www.icm.uu.se
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Re: [gmx-users] Magnetic field in GROMACS

[حبيبة علي]

Dear David and Alex,

Thanks for the replies. I'm happy that you will consider it. You are the
developers and it is clear for you which file should be updated;

Dear Ali,
My coding skills are very bad and I have no idea which file I need to look
at.

Best

On Wed, Jun 20, 2018 at 12:02 PM, Ali Ahmed  wrote:

> Hello,
> I looked for that before and I tried updating the electric field code as
> both of them are related to Lorentz force. Unfortunately, I failed because
> there are different codes need to be updated.
> It would be amazing if the developers participate in this code.
> Thanks
> Ali
>
> On Wed, Jun 20, 2018 at 3:28 AM, David van der Spoel  >
> wrote:
>
> > Den 2018-06-20 kl. 10:20, skrev Alex:
> >
> >> David,
> >>
> >> I can think of many realistic cases when looking at the effects of
> >> magnetic fields in MD would be of interest, just not in what Gromacs is
> >> normally used for.
> >>
> >> It's just a completely different animal in terms of what causes those
> >> effects and Lorentz force applied to point charges would likely be a
> very
> >> bad approximation. But in general, an implementation of self-consistent
> >> MD+FDTD (i.e. MD + Maxwell's eqns) would be pretty amazing.
> >>
> >
> > Feel free to open a redmine issue to discuss it there.
> > We have an implementation of electric fields that can be used as a
> > template.
> >
> >
> >> Alex
> >>
> >>
> >>
> >>> Magnetic fields are typically very weak such that they are negligable
> in
> >>> realistic cases. This is why nobody bothered to implement it.
> >>>
> >>>
> >>
> >
> > --
> > 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.
> > http://www.icm.uu.se
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/Support
> > /Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
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> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
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Department of Chemistry,
University of Mosul-Iraq
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Re: [gmx-users] Continuation of the gromacs job using gmx convert-tpr

[Own 12121325]

and without append flag it will produce an output in the separate file,
won't it?

gmx convert-tpr -s init.tpr -o next.tpr -extend 50
gmx mdrun -s next.tpr -cpi the_last_chekpoint.cpt

2018-06-21 1:12 GMT+02:00 Justin Lemkul :

>
>
> On 6/19/18 4:45 AM, Own 12121325 wrote:
>
>> Hello Justin,
>>
>> could you specify please a bit more. Following your method, if the
>> simulation has been terminated by crash without producing gro file so to
>> re-initiate it I only need one command:
>>
>> gmx mdrun -s initial.tpr -cpi the_last_chekpoint.cpt -append
>>
>> where the last_checkpoint should be something like initial.cpt or
>> initial_prev.cpt
>>
>
> Right.
>
> but In case if my simulation has been finished correctly e.g. for 50 ns and
>> I now need to extend it for another 50 ns,  should I do the following
>> trick
>> with 2 GMX programs:
>>
>> gmx convert-tpr -s init.tpr -o next.tpr -extend 50
>> gmx mdrun -s next.tpr -cpi the_last_chekpoint.cpt -append
>>
>> it will produce the second part of the trajectory as the new file
>> (next.trr) or merge together the first and the second part ?
>>
>
> You're specifying -append, so the output will be concatenated by mdrun.
> That's also been default behavior for as long as I can remember, too :)
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
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Re: [gmx-users] (no subject)

[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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