Re: [gmx-users] how to visualize gromacs trajectory

[Stephani Macalino]

Hi,
Yes that command is right.
If you need to do other commands, the trjconv description and options are
in the second link I gave:
 http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-trjconv.html
Regards,
Stephani

On Tue, 9 Jul 2019 at 00:13, sunyeping  wrote:

> Hello, steph,
>
> I have read the workflow for trajectory fixing at
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions,
> but I don't know how to perform these steps.
> The workflow reads:
>
>1. First make your molecules whole if you want them whole.
>2. Cluster your molecules/particles if you want them clustered.
>3. If you want jumps removed, extract the first frame from the
>trajectory to use as  reference, and then use trjconv -pbc nojump with
>that first frame as reference
>4. Center your system using some criterion. Doing so shifts the
>system, so don't use trjconv -pbc nojump after this step.
>5. Perhaps put everything in some box with the other trjconv -pbc or
> -ur options.
>6. Fit the resulting trajectory to some (other) reference structure
>(if desired), and don't use any PBC related option afterwards.
>
> For the step 1, what this the command for keep the molecule whole? Should
> it be:
>
> gmx trjconv -s md_0_10.tpr -f md_0_10.xtc -o md_0_10_whole.xtc -pbc whole
>  ?
> Could you give me some examples of the command for each step?
>
> Thanks.
>
> Yeping
>
> --
>
> From:孙业平 
> Sent At:2019 Jul. 3 (Wed.) 17:39
> To:gromacs 
> Subject:Re: [gmx-users] how to visualize gromacs trajectory
>
> Hi, Steph
>
> I used the following command to repair the trajectory:
>
>
> gmx trjconv -s md_0_10.tpr -f md_0_10.xtc -o md_0_10_center.xtc -center  -pbc 
> mol -ur compact
>
>
> the bond stretching has disappeared, but the subunits of the protein seperate 
> from each other. How to deal with this? Would it be useful to repeat the 
> trjconv command?
>
> Yeping
>
> --
> From:Stephani Macalino 
> Sent At:2019 Jul. 3 (Wed.) 12:24
> To:gromacs 
> Subject:Re: [gmx-users] how to visualize gromacs trajectory
>
> Hello,
> It sounds like you have to fixed broken molecules and have problem with
> boundary conditions.
> After doing the MD, you need to fix your trajectory first before doing
> visualization.
> Check this link for a workflow:
>
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
>
>
> And this:
> http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-trjconv.html
> for detailed trjconv command options.
> Regards,
> Steph
>
>
> On Wed, 3 Jul 2019 at 12:21, Sun Yeping  wrote:
>
> > Dear all,
> >
> > I wish to know what is the best way to visualize gromacs trajectory.
> >
> > When I load a gromacs trajectory into VMD, I find some of the water
> > molecules and some part of the protein in the system are streched and the
> > structure become weild and cannot be properly analyzed.
> >
>
> > I searched google and found there is a gromacs plugin for vmd, but I don't
> > know whether it will help improve gromcas trajectory visualization (
> >
> >
> https://www.ks.uiuc.edu/Research/vmd/plugins/updates/vmd192_gromacs_update1/
> > ).
> >
> > I also found there is a gromcas plugin for pymol (
> > https://bioexcel.eu/run-gromacs-within-pymol-with-dynamics/
> ). But it seems
>
> > to be used for simulation. It doesn't seem to be used to load and visualize
> > a extraneous the gromacs trajectory.
> >
> > What are your suggestion？ Thank you in advance.
> >
> > Yeping
> > --
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> >
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> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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Re: [gmx-users] POPC Berger lipids parameters for AMBER99sb

[Justin Lemkul]

On 7/8/19 7:31 PM, Carlos Navarro wrote:

Dear gmx-users,
I was wondering if someone can share the Berger parameters for POPC for
Amber99sb (and I they can share also a .pdb .gro file will be even better).
I found several for gromos, but I need them form AMBER99sb.


Berger parameters are united-atom and designed for use with GROMOS. I 
know some people have combined them with various protein force fields 
with varying success, but I would not do that. Berger parameters are 
wildly outdated and much better force fields exist. In your case, use 
Slipids, which are specifically designed to be compatible with AMBER.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
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==

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Re: [gmx-users] Repeat Simulation n times

[Justin Lemkul]

On 7/8/19 1:43 PM, Neena Susan Eappen wrote:

Hello gromacs users,

To repeat a simulation say 50 times, do I manually start from minimization step 
to data collection 50 times, or is there anything I can write in the command 
line?


To run 50 independent simulations, I would run minimization once and 
start from 50 new equilibration runs, each with a different set of 
initial velocities (change gen_seed or simply set to -1).


That approach may not be as robust as starting from 50 different 
configurations, but the exact approach depends on the system in question.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
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Re: [gmx-users] rigid body motion

[Justin Lemkul]

On 7/8/19 11:54 AM, Morteza Chehel Amirani wrote:

Hello,

I'm just wondering what is the best way to put constraints on a group of
molecules (several water molecules + ions) to move as a rigid body i.e., to
keep the relative distance between atoms of the group fixed? The water
molecules and ions form a droplet in my simulation and I would like to
enforce it to remain a droplet throughout the simulation.


GROMACS is not well suited to rigid-body dynamics. Try software like LAMMPS.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

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

==

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Re: [gmx-users] NVT ensemble for simulating of carbon nanotube (as drug delivery)

[Justin Lemkul]

On 7/8/19 3:22 AM, afsaneh maleki wrote:

Hi all
I have two questions:

1-  Is it correct to apply statistical ensemble NVT (N=constant,
T=constant) for simulating of carbon nanotube (as drug delivery)?  It
doesn’t leads to a pressure in the system that is far from normal pressure?
Some Author use VNT and the other use NPT. In the other word, when we can
use NVT ensemble to simulation CNT (as drug delivery)?


The ensemble should be chosen based on which conditions are relevant to 
the simulation. Perhaps some people use NVT simply to side-step any 
possibility of compression along the CNT axis; sometimes models are 
simplified in this way. Perhaps that's not the most accurate. That's 
your job to decide what is the best model for the questions you are 
trying to answer.



2-  How to distinguish between infinite CNT and finite CNT with command
in .mdp file?


The main difference is in the topology, but in the case of an infinite 
CNT, you must use "periodic_molecules = yes" in the .mdp file. Proper 
bonds must be specified in the topology.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

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

==

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Re: [gmx-users] gromacs pullcode

[Justin Lemkul]

On 7/6/19 9:17 PM, zhaox wrote:

Hi,
There are two  groups in my system.When I use the pull code to pull 
one group along the axis X, setting pull_coord1_geometry =direction,I 
am confused with the "distance at start" and the "reference at 
t=0".Could anyone can tell me how to understand these?And if I use the 
absolute reference,how to understand these? For


Reference at t0 refers to the COM position of group1. Distance at start 
is the COM distance between the two groups.


example,when I set the pull_coord1_origin=0 0 0,what means the 
"distance at start"?


This should be the same concept, except that rather than having a 
reference that is the COM of a specified group, it is the coordinate origin.



Thank you in advance.
My pull code is followed:
; Pull code
freezegrps          = bot    top
freezedim           = Y Y Y  N N  N
pull                = yes
pull_ncoords        = 1           ; only one reaction coordinate
pull_ngroups        = 2           ; one group defining one reaction 
coordinate

pull_group1_name    = top
pull_group2_name    = bot
pull_coord1_type    = constant-force
pull_coord1_geometry= direction
;pull_coord1_origin  =
pull_coord1_vec     = 1 0 0
pull_coord1_groups  = 1 2
pull_coord1_start   = yes
;pull_coord1_rate    = -0.0001
pull_coord1_dim     = y n n


Note that pull_coord1_dim is not used with "direction" geometry.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

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

==

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[gmx-users] POPC Berger lipids parameters for AMBER99sb

[Carlos Navarro]

Dear gmx-users,
I was wondering if someone can share the Berger parameters for POPC for
Amber99sb (and I they can share also a .pdb .gro file will be even better).
I found several for gromos, but I need them form AMBER99sb.
Best regards,
Carlos


——
Carlos Navarro Retamal
Bioinformatic Engineering. PhD.
Postdoctoral Researcher in Center of Bioinformatics and Molecular
Simulations
Universidad de Talca
Av. Lircay S/N, Talca, Chile
E: carlos.navarr...@gmail.com or cnava...@utalca.cl
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Re: [gmx-users] About 2019 GMX manual

[Alan]

Dear Benson and Paul,

Thank you both very much. I will open the issue in redmine and, Benson, I'd
appreciate if you could act on my behalf at gerrit.

Best regards,

Alan

On Mon, 8 Jul 2019 at 03:37, Paul bauer  wrote:

> Hello,
>
> as Benson said, please open an issue at redmine.gromacs.org for all
> kinds of bugs that you find :) (even documentation issues like this)!
> After this, you can upload a fix for the issue yourself at
> gerrit.gromacs.org after creating an account there, or one of us will
> get around to do this.
>
> Cheers
>
> Paul
>
> On 07/07/2019 19:59, Benson Muite wrote:
> > Hi Alan,
> >
> > This requires making a small change in the git repository at
> > https://gerrit.gromacs.org
> >
> > The relevant line is also mirrored at:
> >
> >
> https://github.com/gromacs/gromacs/blob/master/docs/user-guide/system-preparation.rst
> >
> >
> > but changes typically go through the git repository at
> > gerrit.gromacs.org as indicated at:
> >
> >
> http://manual.gromacs.org/documentation/current/dev-manual/overview.html#documentation-organization
> >
> >
> > Can make the change on your behalf if it would be helpful.
> >
> > Benson
> >
> > On 7/7/19 8:35 PM, Alan wrote:
> >
> >> Is there a better way to report issues with the current manual?
> >>
> >> It's a very minor one, to update a link about ACPYPE on page 25.
> >>
> >> To use: https://github.com/alanwilter/acpype
> >>
> >> Thanks,
> >>
> >> Alan
>
>
> --
> Paul Bauer, PhD
> GROMACS Release Manager
> KTH Stockholm, SciLifeLab
> 0046737308594
>
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-- 
Wanna help a great cause? Please:
*https://www.raymondnicolettrust.com/events/2019/11/1/pbp2019
*
And many thanks!

Alan ‍♂‍♂
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[gmx-users] Repeat Simulation n times

[Neena Susan Eappen]

Hello gromacs users,

To repeat a simulation say 50 times, do I manually start from minimization step 
to data collection 50 times, or is there anything I can write in the command 
line?

Thank you,
Neena
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Re: [gmx-users] Self-interaction across periodic boundaries

[Salman Zarrini]

Thanks Mark.
The problem is that I would like to keep the overall concentration
constant, so, using a larger box e.g. with 2 times larger lateral box
dimensions,
needs me to increase the number of molecules 8 times, so even more likely
to lead to percolating structures in a larger simulation box.

Best regards,
Salman Zarrini

On Mon, Jul 8, 2019 at 6:24 AM Mark Abraham 
wrote:

> Hi,
>
> If you're trying to model something like it was at infinite dilution using
> a periodic box, then the size of the box needs to be at least as large as
> the size of the structure and its effective interaction radius. It seems
> like your simulation is suggesting at least one of those is larger than you
> first thought it was :-)
>
> Mark
>
> On Mon, 8 Jul 2019 at 11:58, Salman Zarrini 
> wrote:
>
> > Dear all,
> > Using MD simulations I expect to observe aggregation among some molecules
> > solvated in water to have ultimately a droplet out of the molecules. The
> > aggregates form to some extent in the course of simulation time, however,
> > after a while the system become kinetically trapped in artificial
> > percolating aggregates in which the molecules are self-interacting across
> > the periodic boundaries.
> > I wonder if there is any possibility to prevent aggregates
> self-interaction
> > across periodic boundaries?
> >
> > Thank you,
> > Salman
> > --
> > Best regards,
> >
> > Salman Zarrini
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[gmx-users] rigid body motion

[Morteza Chehel Amirani]

Hello,

I'm just wondering what is the best way to put constraints on a group of
molecules (several water molecules + ions) to move as a rigid body i.e., to
keep the relative distance between atoms of the group fixed? The water
molecules and ions form a droplet in my simulation and I would like to
enforce it to remain a droplet throughout the simulation.

Sincerely,
Morteza
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Re: [gmx-users] how to visualize gromacs trajectory

[sunyeping]

Hello, steph,

I have read the workflow for trajectory fixing at 
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions, 
but I don't know how to perform these steps.
The workflow reads:

First make your molecules whole if you want them whole.
Cluster your molecules/particles if you want them clustered.
If you want jumps removed, extract the first frame from the trajectory to use 
as  reference, and then use trjconv -pbc nojump with that first frame as 
reference
Center your system using some criterion. Doing so shifts the system, so don't 
use trjconv -pbc nojump after this step.
Perhaps put everything in some box with the other trjconv -pbc or -ur options.
Fit the resulting trajectory to some (other) reference structure (if desired), 
and don't use any PBC related option afterwards.
For the step 1, what this the command for keep the molecule whole? Should it be:
  gmx trjconv -s md_0_10.tpr -f md_0_10.xtc -o md_0_10_whole.xtc -pbc whole 
  ?
Could you give me some examples of the command for each step?

Thanks.

Yeping

--

From:孙业平 
Sent At:2019 Jul. 3 (Wed.) 17:39
To:gromacs 
Subject:Re: [gmx-users] how to visualize gromacs trajectory

Hi, Steph

I used the following command to repair the trajectory:

gmx trjconv -s md_0_10.tpr -f md_0_10.xtc -o md_0_10_center.xtc -center  -pbc 
mol -ur compact

the bond stretching has disappeared, but the subunits of the protein seperate 
from each other. How to deal with this? Would it be useful to repeat the 
trjconv command?

Yeping

--
From:Stephani Macalino 
Sent At:2019 Jul. 3 (Wed.) 12:24
To:gromacs 
Subject:Re: [gmx-users] how to visualize gromacs trajectory

Hello,
It sounds like you have to fixed broken molecules and have problem with
boundary conditions.
After doing the MD, you need to fix your trajectory first before doing
visualization.
Check this link for a workflow:
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions


And this:
http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-trjconv.html
for detailed trjconv command options.
Regards,
Steph


On Wed, 3 Jul 2019 at 12:21, Sun Yeping  wrote:

> Dear all,
>
> I wish to know what is the best way to visualize gromacs trajectory.
>
> When I load a gromacs trajectory into VMD, I find some of the water
> molecules and some part of the protein in the system are streched and the
> structure become weild and cannot be properly analyzed.
>
> I searched google and found there is a gromacs plugin for vmd, but I don't
> know whether it will help improve gromcas trajectory visualization (
>
> https://www.ks.uiuc.edu/Research/vmd/plugins/updates/vmd192_gromacs_update1/
> ).
>
> I also found there is a gromcas plugin for pymol (
> https://bioexcel.eu/run-gromacs-within-pymol-with-dynamics/). But it seems
> to be used for simulation. It doesn't seem to be used to load and visualize
> a extraneous the gromacs trajectory.
>
> What are your suggestion？ Thank you in advance.
>
> Yeping
> --
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Re: [gmx-users] Self-interaction across periodic boundaries

[Mark Abraham]

Hi,

If you're trying to model something like it was at infinite dilution using
a periodic box, then the size of the box needs to be at least as large as
the size of the structure and its effective interaction radius. It seems
like your simulation is suggesting at least one of those is larger than you
first thought it was :-)

Mark

On Mon, 8 Jul 2019 at 11:58, Salman Zarrini 
wrote:

> Dear all,
> Using MD simulations I expect to observe aggregation among some molecules
> solvated in water to have ultimately a droplet out of the molecules. The
> aggregates form to some extent in the course of simulation time, however,
> after a while the system become kinetically trapped in artificial
> percolating aggregates in which the molecules are self-interacting across
> the periodic boundaries.
> I wonder if there is any possibility to prevent aggregates self-interaction
> across periodic boundaries?
>
> Thank you,
> Salman
> --
> Best regards,
>
> Salman Zarrini
> --
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[gmx-users] Self-interaction across periodic boundaries

[Salman Zarrini]

Dear all,
Using MD simulations I expect to observe aggregation among some molecules
solvated in water to have ultimately a droplet out of the molecules. The
aggregates form to some extent in the course of simulation time, however,
after a while the system become kinetically trapped in artificial
percolating aggregates in which the molecules are self-interacting across
the periodic boundaries.
I wonder if there is any possibility to prevent aggregates self-interaction
across periodic boundaries?

Thank you,
Salman
-- 
Best regards,

Salman Zarrini
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Re: [gmx-users] Install on Windows 10 with AMD GPU

[James Burchfield]

Thankyou Szilárd,
Headers are available here https://github.com/KhronosGroup/OpenCL-Headers
But I get
CMake Error at cmake/gmxManageOpenCL.cmake:45 (message):
  OpenCL is not supported.  OpenCL version 1.2 or newer is required.
Call Stack (most recent call first):
  CMakeLists.txt:236 (include)

I am setting 
OpenCL_include_DIR to C:/Users/Admin/ OpenCL-Headers-master/CL
OpenCL_INCLUDE_DIR OpenCL_Library to C:/Windows/System32/OpenCL.dll


The error file includes 
  Microsoft (R) C/C++ Optimizing Compiler Version 19.21.27702.2 for x64

  CheckSymbolExists.c

  Copyright (C) Microsoft Corporation.  All rights reserved.

  cl /c /Zi /W3 /WX- /diagnostics:column /Od /Ob0 /D WIN32 /D _WINDOWS /D 
"CMAKE_INTDIR=\"Debug\"" /D _MBCS /Gm- /RTC1 /MDd /GS /fp:precise /Zc:wchar_t 
/Zc:forScope /Zc:inline /Fo"cmTC_2c430.dir\Debug\\" 
/Fd"cmTC_2c430.dir\Debug\vc142.pdb" /Gd /TC /errorReport:queue "C:\Program 
Files\gromacs\CMakeFiles\CMakeTmp\CheckSymbolExists.c"

C:\Program Files\gromacs\CMakeFiles\CMakeTmp\CheckSymbolExists.c(2,10): error 
C1083:  Cannot open include file: 'OpenCL_INCLUDE_DIR-NOTFOUND/CL/cl.h': No 
such file or directory [C:\Program 
Files\gromacs\CMakeFiles\CMakeTmp\cmTC_2c430.vcxproj]


File C:/Program Files/gromacs/CMakeFiles/CMakeTmp/CheckSymbolExists.c:
/* */
#include 

int main(int argc, char** argv)
{
  (void)argv;
#ifndef CL_VERSION_1_0
  return ((int*)(_VERSION_1_0))[argc];
#else
  (void)argc;
  return 0;
#endif
}


Guessing it is time to give up

Cheers
James




-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 On Behalf Of Szilárd Páll
Sent: Friday, 5 July 2019 10:20 PM
To: Discussion list for GROMACS users 
Cc: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Install on Windows 10 with AMD GPU

Dear James,

Unfortunately, we have very little experience with OpenCL on Windows, so I am 
afraid I can not advise you on specifics. However, note that the only part of 
the former SDK that is needed is the OpenCL headers and loader libraries 
(libOpenCL) which is open source software that can be obtained from the 
standards body, KHronos. Not sure what the mechanism is for Windows, but for 
Linux these components are in packaged in the standard repositories of most 
distributions.

However, before going through a large effort of trying to get GROMACS running 
on Windows + AMD + OpenCL, you might want to consider evaluating the potential 
benefits of the hardware. As these cards are quite dated you might find that 
they do not provide enough performance benefit to warrant the effort required 
-- especially as, if you have a workstation with significant CPU resources, you 
might find that GROMACS runs nearly as fast or faster on the CPU only (that's 
because we have very efficient CPU SIMD code for all compute-intensive work).

To do a hopefully easier quick performance evaluation, you could simply boot a 
Linux distribution off of an external disk, you can find Linux drivers for them 
for Ubuntu 16.04/18.04 at least which you can install and see how well does the 
system perform.

I hope that helps!

Cheers,
--
Szilárd


On Fri, Jul 5, 2019 at 9:11 AM James Burchfield < 
james.burchfi...@sydney.edu.au> wrote:

> Hi there,
>
> I was hoping to install  gromacs on a windows10 system that runs 2 AMD 
> Firepro cards.
> I have managed to achieve almost everything in terms of setting up the 
> compilation with the exception of OpenCl.
>
> The issue I have run into are in reference to the settings of
>
> CMAKE_PREFIX_PATH  (unsure if I need to put anything here) 
> OpenCL_INCLUDE_DIR OpenCL_Library
>
> The cards I am running are~ 5years old Firepro W7100 OpenCL version 
> they are running is 2.0
>
>
> AMD no longer makes the OpenCL SDK
> Apparrently, most of the relevant stuff is now included with the 
> drivers and headers can be  downloaded from GitHub
>
> I have tried
>
>   *   Installing the old SDK
>   *   Installing the newer "light" version of the SDK
>   *   Downloading the headers
>
> Whatever the case
> I cannot get it to work .
> I get an error saying that the minimum requirement is openCl 1.2.
> According to the AMD driver the cards are running opencl 2.0
>
> Any help would be appreciated
>
> Cheers,
> James
>
>
> 
> Dr James Burchfield
> Group Leader - Molecular Imaging
> Metabolic Cybernetics Laboratory | School of Life and Environmental 
> Sciences
> D17 - Charles Perkins Centre | The University of Sydney | NSW | 2006
> email: james.burchfi...@sydney.edu.au< 
> https://protect-au.mimecast.com/s/gzn3CGvmB5ilERGxIKvKhT?domain=webmai
> l.sydney.edu.au
> >
> phone: +61 (0) 403 977 448
> web: 
> http://sydney.edu.au/perkins/research/groups/david-james-lab.shtml
> 
>
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> 

Re: [gmx-users] About 2019 GMX manual

[Paul bauer]

Hello,

as Benson said, please open an issue at redmine.gromacs.org for all 
kinds of bugs that you find :) (even documentation issues like this)!
After this, you can upload a fix for the issue yourself at 
gerrit.gromacs.org after creating an account there, or one of us will 
get around to do this.


Cheers

Paul

On 07/07/2019 19:59, Benson Muite wrote:

Hi Alan,

This requires making a small change in the git repository at 
https://gerrit.gromacs.org


The relevant line is also mirrored at:

https://github.com/gromacs/gromacs/blob/master/docs/user-guide/system-preparation.rst 



but changes typically go through the git repository at 
gerrit.gromacs.org as indicated at:


http://manual.gromacs.org/documentation/current/dev-manual/overview.html#documentation-organization 



Can make the change on your behalf if it would be helpful.

Benson

On 7/7/19 8:35 PM, Alan wrote:


Is there a better way to report issues with the current manual?

It's a very minor one, to update a link about ACPYPE on page 25.

To use: https://github.com/alanwilter/acpype

Thanks,

Alan



--
Paul Bauer, PhD
GROMACS Release Manager
KTH Stockholm, SciLifeLab
0046737308594

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