Re: [gmx-users] Is Gromos force fields not recommended?

[Bratin Kumar Das]

It is not like that...gromos is not compatible with gromacs... decission
need to be taken depending on what system you want to simulate and what you
are expecting from the simulation.
On Tue 18 Feb, 2020, 6:27 AM Myunggi Yi,  wrote:

> Dear users,
>
> As the same as the title,
>
> Are Gromos force fields not recommended in Gromacs?
> --
> 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.

Re: [gmx-users] Is Gromos force fields not recommended?

[Mark Abraham]

Hi,

No. Why do you ask?

Mark

On Tue., 18 Feb. 2020, 01:57 Myunggi Yi,  wrote:

> Dear users,
>
> As the same as the title,
>
> Are Gromos force fields not recommended in Gromacs?
> --
> 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.

Re: [gmx-users] Keeping more than 1 version of gromacs on single os UBUNTU

[Navneet Kumar]

Thank you, Sir!

On Mon, Feb 17, 2020 at 8:16 PM Christian Blau  wrote:

> Hi Navneet,
>
> This is achieved by setting the installation directory with cmake for the
> respective source code that you downloaded, then sourcing different GMXRC.
>
> Install different GROMACS builds fromt the source code into seperate
> folders using something like
>
> -DCMAKE_INSTALL_PREFIX=/home/navneet/local/gromacs-2019.6
>
> and for another version
>
> -DCMAKE_INSTALL_PREFIX=/home/navneet/local/gromacs-2020
>
> Then,
>
> "source /home/navneet/local/gromacs-2020/bin/GMXRC"
>
> will give you GROMACS 2020, while
>
> "source /home/navneet/local/gromacs-2019.6/bin/GMXRC"
>
> will give you GROMACS2019.6.
>
> Best,
>
> Christian
>
> On 2020-02-17 15:15, Navneet Kumar wrote:
> > Hello Everyone!
> >
> > I have currently installed GROMACS 2018.8 and using it. But for some of
> my
> > previous work, I want to use the older version of GROMACS i.e 5.x.
> > I have installed the GROMACS using this method
> >
> >> sudo cmake .. -DGMX_BUILD_OWN_FFTW=OFF -DREGRESSIONTEST_DOWNLOAD=OFF
> > -DCMAKE_C_COMPILER=/usr/bin/gcc-6
> > -DREGRESSIONTEST_PATH=/home/nitttr/Downloads/regressiontests-2018.8
> >> everytime when I use GROMACS I start with command-
> > "source /usr/local/gromacs/bin/GMXRC"
> > How can I install some other version of gromacs and use simultaneously?
> >
> >
> > /
> --
> 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.
>


-- 






 Thanks & Regards
___

[image: photo]
*NAVNEET KUMAR*
Doctoral Student
Dept. of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research, Sector 67,
S.A.S. Nagar - 160062, Punjab (INDIA)
P +918017967647  <+918017967647> |
E navneet...@gmail.com  

 

Please consider your environmental responsibility. Before printing this
e-mail message, ask yourself whether you really need a hard copy.
-- 
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] How to dynamically change the "pull-coord1-init" during SMD simulation

[bonjour899]

Hello everyone,


This email is asking for some suggestions. Actually I'd like to conduct a kind 
of steered molecular dynamics simulation like this:
Fixing one end of a protein, pulling the other end for a certain distance Δx 
(can be for example 0.5 nm, 0.2 nm ...), relaxing the whole system for 
sufficient time and then repeating that.
The method I can think of is still using COM pulling code
pull-coord1-type=umbrella
pull-coord1-geometry=diatance
This is like applying a harmonic spring between the two ends of the protein 
with harmonic potential U=1/2*k*(r-r0)^2 and I think I should modify the 
parameter "pull-coord1-init" to extend the equilibrium length of the spring for 
Δx so that I can achieve pulling the protein for Δx (is "pull-coord1-init" like 
the r0 in the harmonic potential equation? Maybe my understanding of this 
parameter is wrong?).
However, since I want to pull the protein for a long distance, I should 
gradually change the equilibrium length, and I have no idea how to dynamically 
change the "pull-coord1-init" during SMD simulation. Or do I have to restart 
the simulation with a new .mdp file with different "pull-coord1-init" for each 
step?


Best regards,
W
-- 
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] Is Gromos force fields not recommended?

[Myunggi Yi]

Dear users,

As the same as the title,

Are Gromos force fields not recommended in Gromacs?
-- 
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] Increase Graphene sheet size

[Dallas Warren]

genconf will only stack the box that you have in the original box in
integer values.

i.e. -nbox 2 4 10

If want a specific dimension, then the box you are stacking has to be an
integer fraction of the final dimensions.

Also note that the final dimension also has to be possible with the
inter-atomic distances for the carbon atoms that make up the sheet.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Mon, 17 Feb 2020 at 21:11, Mohamed Abdelaal 
wrote:

> Hello All,
>
> I want to create a graphene sheet with a specific dimensions (10*15*0.284)
> nm.
>
> I created a .gro file as below ( as mentioned in this website
>
> https://erastova.xyz/teaching/practical-simulations-for-molecules-and-materials/material-simulations/graphene-simulation-set-up/
> )
>
> GRM: 1 1 Rcc=1.420 Rhole=0.000 Center: Ring
> 4
> 1GRM   C1  1   0.061   0.071   0.000
> 1GRM   C2  2   0.184   0.142   0.000
> 1GRM   C3  3   0.184   0.284   0.000
> 1GRM   C4  4   0.061   0.355   0.000
> 0.2459510.4260000.284000
>
> Now I don't know how to use genconf to repeat it until it gives me the
> required dimensions. As using genconf -nbox will repeat the above into a
> specific number of boxes but I can't get a sheet with accurate dimensions
> of (10*15*0.284 nm).
>
> I tried to generate a sheet using gencong and then use editconf to change
> the dimensions to the required ones, but the problem is that using editconf
> will put the graphene sheet in an empty box but will not change the
> dimension as I want.
>
> Another option is to divide the 10 (the required dimension) nm by 0.245951
> (the dimension in the above .gro file) and to use the genconf with the
> result but it will be a lot of decimals and I am not sure if it will also
> give me the accurate dimension.
>
> Can anybody help me or guide me how to solve that problem.
>
> Thanks,
> Mohamed
> --
> 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] Fwd: Compiling with OpenCL for Macbook AMD Radeon Pro 560 GPU

[Oliver Dutton]

Hello,

I am trying to do the exact same as Michael in 
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2019-February/124394.html
 

 but hit the exact same error of it not finding a simple header file. I’ve 
tried building 2019.5 and 2020 Gromacs on a MacBook Pro with AMD Radeon Pro 560 
GPU. 

I’m using the apple inbuilt compiler, same flags and cmake options as Michael. 
Was this ever got working?

Kind regards,
Oliver

-- 
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] How to set restraints in free energy calculation?

[Sadaf Rani]

Dear Gromacs users
I am doing a free energy calculation of the protein-ligand complex. During
decoupling of the ligand vdw forces from protein, I have selected 21
different lambda windows between 0-1.
I have put distance angle and dihedral restraints to keep the ligand in its
position but in some of my lamda windows, the residue restrained with
ligand crashes and generates different PDB structures. The residue of
protein on which I put restraints for ligand brreaks apart and simulation
crashes in lambda windows 0,1,2,4,8,9,11,12,13,17,18 however in windows
3,5,6,10, 14,15,19,20 it works well.
My restraint section in topology is as below:-

; distance restraints
[ bonds ]
;i j  type r0A r1A r2AfcAr0B r1B r2B
 fcB
  3437  790810 0.474   0.474   10.0   0.00.474   0.474   10.0
4184.000

[ angle_restraints ]
;   aiajakal  typethA  fcAmultA  thB  fcB
 multB
  3437  7908  7905  7908   1110.00   0.01 110.0041.840
  1
  7908  3437  3439  3437   1152.50.01 152.5 41.840
  1

[ dihedral_restraints ]
;   aiajakal   typephiAdphiA  fcAphiB  dphiB
 fcB
  7905  7908  3437  3439 1140.19   0.00.0140.190.0
 41.840
  7909  7908  3437  3439 1-167.75  0.00.0-69.050.0
 41.840
  7909  7908  3437  3433 1-172.77  0.00.0   -172.770.0
 41.840


Can anyone please suggest me how should I fix this? or where I am doing
wrong?
I will be really grateful.

Thanks.

Sadaf Rani
P.hD. visiting scholar
Lancaster University
Uk
-- 
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] REMD stall out

[Daniel Burns]

Thanks Mark and Szilard,

I forwarded Mark's suggestion to IT.  I'll see what they have to say and
then I'll try the simulation again and open an issue on redime.

Thank you,

Dan

On Mon, Feb 17, 2020 at 9:09 AM Mark Abraham 
wrote:

> Hi,
>
> That could be caused by configuration of the parallel file system or MPI on
> your cluster. If only one file descriptor is available per node to an MPI
> job, then your symptoms are explained. Some kinds of compute jobs follow
> such a model, so maybe someone optimized something for that.
>
> Mark
>
> On Mon, 17 Feb 2020 at 15:56, Daniel Burns  wrote:
>
> > HI Szilard,
> >
> > I've deleted all my output but all the writing to the log and console
> stops
> > around the step noting the domain decomposition (or other preliminary
> > task).  It is the same with or without Plumed - the TREMD with Gromacs
> only
> > was the first thing to present this issue.
> >
> > I've discovered that if each replica is assigned its own node, the
> > simulations proceed.  If I try to run several replicas on each node
> > (divided evenly), the simulations stall out before any trajectories get
> > written.
> >
> > I have tried many different -np and -ntomp options as well as several
> slurm
> > job submission scripts with node/ thread configurations but multiple
> > simulations per node will not work.  I need to be able to run several
> > replicas on the same node to get enough data since it's hard to get more
> > than 8 nodes (and as a result, replicas).
> >
> > Thanks for your reply.
> >
> > -Dan
> >
> > On Tue, Feb 11, 2020 at 12:56 PM Daniel Burns 
> wrote:
> >
> > > Hi,
> > >
> > > I continue to have trouble getting an REMD job to run.  It never makes
> it
> > > to the point that it generates trajectory files but it never gives any
> > > error either.
> > >
> > > I have switched from a large TREMD with 72 replicas to the Plumed
> > > Hamiltonian method with only 6 replicas.  Everything is now on one node
> > and
> > > each replica has 6 cores.  I've turned off the dynamic load balancing
> on
> > > this attempt per the recommendation from the Plumed site.
> > >
> > > Any ideas on how to troubleshoot?
> > >
> > > Thank you,
> > >
> > > Dan
> > >
> > --
> > 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.
>
-- 
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] REMD stall out

[Mark Abraham]

Hi,

That could be caused by configuration of the parallel file system or MPI on
your cluster. If only one file descriptor is available per node to an MPI
job, then your symptoms are explained. Some kinds of compute jobs follow
such a model, so maybe someone optimized something for that.

Mark

On Mon, 17 Feb 2020 at 15:56, Daniel Burns  wrote:

> HI Szilard,
>
> I've deleted all my output but all the writing to the log and console stops
> around the step noting the domain decomposition (or other preliminary
> task).  It is the same with or without Plumed - the TREMD with Gromacs only
> was the first thing to present this issue.
>
> I've discovered that if each replica is assigned its own node, the
> simulations proceed.  If I try to run several replicas on each node
> (divided evenly), the simulations stall out before any trajectories get
> written.
>
> I have tried many different -np and -ntomp options as well as several slurm
> job submission scripts with node/ thread configurations but multiple
> simulations per node will not work.  I need to be able to run several
> replicas on the same node to get enough data since it's hard to get more
> than 8 nodes (and as a result, replicas).
>
> Thanks for your reply.
>
> -Dan
>
> On Tue, Feb 11, 2020 at 12:56 PM Daniel Burns  wrote:
>
> > Hi,
> >
> > I continue to have trouble getting an REMD job to run.  It never makes it
> > to the point that it generates trajectory files but it never gives any
> > error either.
> >
> > I have switched from a large TREMD with 72 replicas to the Plumed
> > Hamiltonian method with only 6 replicas.  Everything is now on one node
> and
> > each replica has 6 cores.  I've turned off the dynamic load balancing on
> > this attempt per the recommendation from the Plumed site.
> >
> > Any ideas on how to troubleshoot?
> >
> > Thank you,
> >
> > Dan
> >
> --
> 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.

Re: [gmx-users] REMD stall out

[Szilárd Páll]

Hi Dan,

What you describe in not an expected behaviro and it is something we should
look into.

What GROMACS version were you using? One thing that may help diagnosing the
issue is: try to disable replica exchange and run -multidir that way. Does
the simulation proceed?

Can you please open an issue on redmine.gromacs.org and upload the
necessary input files to reproduce, logs of your runs that reproduced the
issue.

Cheers,
--
Szilárd


On Mon, Feb 17, 2020 at 3:56 PM Daniel Burns  wrote:

> HI Szilard,
>
> I've deleted all my output but all the writing to the log and console stops
> around the step noting the domain decomposition (or other preliminary
> task).  It is the same with or without Plumed - the TREMD with Gromacs only
> was the first thing to present this issue.
>
> I've discovered that if each replica is assigned its own node, the
> simulations proceed.  If I try to run several replicas on each node
> (divided evenly), the simulations stall out before any trajectories get
> written.
>
> I have tried many different -np and -ntomp options as well as several slurm
> job submission scripts with node/ thread configurations but multiple
> simulations per node will not work.  I need to be able to run several
> replicas on the same node to get enough data since it's hard to get more
> than 8 nodes (and as a result, replicas).
>
> Thanks for your reply.
>
> -Dan
>
> On Tue, Feb 11, 2020 at 12:56 PM Daniel Burns  wrote:
>
> > Hi,
> >
> > I continue to have trouble getting an REMD job to run.  It never makes it
> > to the point that it generates trajectory files but it never gives any
> > error either.
> >
> > I have switched from a large TREMD with 72 replicas to the Plumed
> > Hamiltonian method with only 6 replicas.  Everything is now on one node
> and
> > each replica has 6 cores.  I've turned off the dynamic load balancing on
> > this attempt per the recommendation from the Plumed site.
> >
> > Any ideas on how to troubleshoot?
> >
> > Thank you,
> >
> > Dan
> >
> --
> 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.

Re: [gmx-users] REMD stall out

[Daniel Burns]

HI Szilard,

I've deleted all my output but all the writing to the log and console stops
around the step noting the domain decomposition (or other preliminary
task).  It is the same with or without Plumed - the TREMD with Gromacs only
was the first thing to present this issue.

I've discovered that if each replica is assigned its own node, the
simulations proceed.  If I try to run several replicas on each node
(divided evenly), the simulations stall out before any trajectories get
written.

I have tried many different -np and -ntomp options as well as several slurm
job submission scripts with node/ thread configurations but multiple
simulations per node will not work.  I need to be able to run several
replicas on the same node to get enough data since it's hard to get more
than 8 nodes (and as a result, replicas).

Thanks for your reply.

-Dan

On Tue, Feb 11, 2020 at 12:56 PM Daniel Burns  wrote:

> Hi,
>
> I continue to have trouble getting an REMD job to run.  It never makes it
> to the point that it generates trajectory files but it never gives any
> error either.
>
> I have switched from a large TREMD with 72 replicas to the Plumed
> Hamiltonian method with only 6 replicas.  Everything is now on one node and
> each replica has 6 cores.  I've turned off the dynamic load balancing on
> this attempt per the recommendation from the Plumed site.
>
> Any ideas on how to troubleshoot?
>
> Thank you,
>
> Dan
>
-- 
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] Keeping more than 1 version of gromacs on single os UBUNTU

[Christian Blau]

Hi Navneet,

This is achieved by setting the installation directory with cmake for the 
respective source code that you downloaded, then sourcing different GMXRC.

Install different GROMACS builds fromt the source code into seperate folders 
using something like

-DCMAKE_INSTALL_PREFIX=/home/navneet/local/gromacs-2019.6

and for another version

-DCMAKE_INSTALL_PREFIX=/home/navneet/local/gromacs-2020

Then,

"source /home/navneet/local/gromacs-2020/bin/GMXRC"

will give you GROMACS 2020, while

"source /home/navneet/local/gromacs-2019.6/bin/GMXRC"

will give you GROMACS2019.6.

Best,

Christian

On 2020-02-17 15:15, Navneet Kumar wrote:

Hello Everyone!

I have currently installed GROMACS 2018.8 and using it. But for some of my
previous work, I want to use the older version of GROMACS i.e 5.x.
I have installed the GROMACS using this method


sudo cmake .. -DGMX_BUILD_OWN_FFTW=OFF -DREGRESSIONTEST_DOWNLOAD=OFF

-DCMAKE_C_COMPILER=/usr/bin/gcc-6
-DREGRESSIONTEST_PATH=/home/nitttr/Downloads/regressiontests-2018.8

everytime when I use GROMACS I start with command-

"source /usr/local/gromacs/bin/GMXRC"
How can I install some other version of gromacs and use simultaneously?


/

--
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] CGENFF validation / optimization

[Adarsh V. K.]

Dear all,

While suing CGENFF server for " *.str " file generation, Few of the
penalties were found to higher than 50. How to do validation/optimization.?
Is there any recommended softwares / servers available for

* " extensive validation / optimization." or any standard procedure
available to do validation / optimization ?The *.str file also contains the
following message.*

! "penalty" is the highest penalty score of the associated parameters.
! Penalties lower than 10 indicate the analogy is fair; penalties between 10
! and 50 mean some basic validation is recommended; penalties higher than
! 50 indicate poor analogy and mandate extensive validation/optimization.
-
-- 
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] (no subject)

[shakira shukoor]

Thanks christian for the detailed description.

On Mon, Feb 17, 2020 at 8:00 PM Christian Blau  wrote:

> Hi Shakkira,
>
>
> The simulation box deformation is described by six parameters that
> describe three basis box vectors with the following
> contraints,
>
>   - the first box vector is aligned along the x-axis, with coordinates
> thus has coordinates (xx,0,0)
>
>   - the second box vector is aligned in the x-y plane with coordinates
> (yx,yy,0)
>
>   - the third box vector is free (zx,zy,zz)
>
>
> The six parameters that you give in .mdp files are in the following order
>
> xx, yy, zz, yx, zx, zy
>
>
> The corrent box is then calculated as
>
> box(t_start)+(t-t_start)*deform
>
>
> For more information have a look at the gromacs manual mdp parameter
> description:
>
> http://manual.gromacs.org/current/user-guide/mdp-options.html
>
> under non-equilibrium MD:
>
> (0 0 0 0 0 0) [nm ps\ :sup:`-1`]
> The velocities of deformation for the box elements: a(x) b(y) c(z)
> b(x) c(x) c(y). Each step the box elements for which :mdp:`deform`
> is non-zero are calculated as: box(ts)+(t-ts)*deform, off-diagonal
> elements are corrected for periodicity. The coordinates are
> transformed accordingly. Frozen degrees of freedom are (purposely)
> also transformed. The time ts is set to t at the first step and at
> steps at which x and v are written to trajectory to ensure exact
> restarts. Deformation can be used together with semiisotropic or
> anisotropic pressure coupling when the appropriate
> compressibilities are set to zero. The diagonal elements can be
> used to strain a solid. The off-diagonal elements can be used to
> shear a solid or a liquid.
>
>
> Best,
>
> Christian
>
> On 2020-02-16 12:12, shakira shukoor wrote:
> >Hi all
> > Can anyone help me with the DEFORM option in Gromacs to change the box
> > values?
> >
> >
> --
> 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.



-- 
*Best Regards*

Shakkira E
PhD student INSPIRE Scholar
Department of Chemistry
sdmdlab.xyz
IIT Patna
Bihta
Patna 801106
-- 
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] (no subject)

[Christian Blau]

Hi Shakkira,


The simulation box deformation is described by six parameters that describe three basis box vectors with the following 
contraints,


 - the first box vector is aligned along the x-axis, with coordinates thus has 
coordinates (xx,0,0)

 - the second box vector is aligned in the x-y plane with coordinates (yx,yy,0)

 - the third box vector is free (zx,zy,zz)


The six parameters that you give in .mdp files are in the following order

xx, yy, zz, yx, zx, zy


The corrent box is then calculated as

box(t_start)+(t-t_start)*deform


For more information have a look at the gromacs manual mdp parameter 
description:

http://manual.gromacs.org/current/user-guide/mdp-options.html

under non-equilibrium MD:

   (0 0 0 0 0 0) [nm ps\ :sup:`-1`]
   The velocities of deformation for the box elements: a(x) b(y) c(z)
   b(x) c(x) c(y). Each step the box elements for which :mdp:`deform`
   is non-zero are calculated as: box(ts)+(t-ts)*deform, off-diagonal
   elements are corrected for periodicity. The coordinates are
   transformed accordingly. Frozen degrees of freedom are (purposely)
   also transformed. The time ts is set to t at the first step and at
   steps at which x and v are written to trajectory to ensure exact
   restarts. Deformation can be used together with semiisotropic or
   anisotropic pressure coupling when the appropriate
   compressibilities are set to zero. The diagonal elements can be
   used to strain a solid. The off-diagonal elements can be used to
   shear a solid or a liquid.


Best,

Christian

On 2020-02-16 12:12, shakira shukoor wrote:

   Hi all
Can anyone help me with the DEFORM option in Gromacs to change the box
values?



--
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] Keeping more than 1 version of gromacs on single os UBUNTU

[Navneet Kumar]

Hello Everyone!

I have currently installed GROMACS 2018.8 and using it. But for some of my
previous work, I want to use the older version of GROMACS i.e 5.x.
I have installed the GROMACS using this method

>sudo cmake .. -DGMX_BUILD_OWN_FFTW=OFF -DREGRESSIONTEST_DOWNLOAD=OFF
-DCMAKE_C_COMPILER=/usr/bin/gcc-6
-DREGRESSIONTEST_PATH=/home/nitttr/Downloads/regressiontests-2018.8
> everytime when I use GROMACS I start with command-
"source /usr/local/gromacs/bin/GMXRC"
How can I install some other version of gromacs and use simultaneously?


-- 






 Thanks & Regards
___

[image: photo]
*NAVNEET KUMAR*
Doctoral Student
Dept. of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research, Sector 67,
S.A.S. Nagar - 160062, Punjab (INDIA)
P +918017967647  <+918017967647> |
E navneet...@gmail.com  

 

Please consider your environmental responsibility. Before printing this
e-mail message, ask yourself whether you really need a hard copy.
-- 
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] REMD stall out

[Szilárd Páll]

Hi,

If I understand correctly your jobs stall, what is in the log output? What
about the console? Does this happen without PLUMED?

--
Szilárd


On Tue, Feb 11, 2020 at 7:56 PM Daniel Burns  wrote:

> Hi,
>
> I continue to have trouble getting an REMD job to run.  It never makes it
> to the point that it generates trajectory files but it never gives any
> error either.
>
> I have switched from a large TREMD with 72 replicas to the Plumed
> Hamiltonian method with only 6 replicas.  Everything is now on one node and
> each replica has 6 cores.  I've turned off the dynamic load balancing on
> this attempt per the recommendation from the Plumed site.
>
> Any ideas on how to troubleshoot?
>
> Thank you,
>
> Dan
> --
> 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.

Re: [gmx-users] Protein-Ligand Interaction calculation

[Justin Lemkul]

On 2/17/20 7:18 AM, Peter Mawanga wrote:

Hello everyone

I used the CHARMM-GUI Membrane Builder to build a bilayer around my
protein-ligand complex.

However, unfortunately the ligand was not mentioned separately in the index
(.ndx) file although it was mentioned in the topology (.top) file. Hence I
am not able to calculate the energy between the protein and ligand using
the energy (.edr) file.

Please let me know if there is any workaround for this. It would be
difficult to repeat the simulations again.




Computing interaction energy is a post-processing task. You should not 
specify energygrps in your .mdp file for the actual simulation because 
(1) it slows the simulation down and (2) it's not compatible with GPUs.


All you need to do is generate a new .tpr file with the desired 
energygrps (you don't even need a special index file because all 
non-standard [moleculetype] entries are by default assigned to their own 
index groups) and use mdrun -rerun on the existing trajectory and the 
new .tpr file with energygrps.


-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

==

--
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] Protein-Ligand Interaction calculation

[Bratin Kumar Das]

Hi..
  You have to specify energy groups in .mdp option..then rerun the
simulation..and analyse with gmx energy command

On Mon 17 Feb, 2020, 5:52 PM Александр Лашков,  wrote:

> You can rebuild index file using gmx make_ndx gromacs util.
> Alex
>
> пн, 17 февр. 2020 г. в 15:19, Peter Mawanga  >:
>
> > Hello everyone
> >
> > I used the CHARMM-GUI Membrane Builder to build a bilayer around my
> > protein-ligand complex.
> >
> > However, unfortunately the ligand was not mentioned separately in the
> index
> > (.ndx) file although it was mentioned in the topology (.top) file. Hence
> I
> > am not able to calculate the energy between the protein and ligand using
> > the energy (.edr) file.
> >
> > Please let me know if there is any workaround for this. It would be
> > difficult to repeat the simulations again.
> >
> >
> > --
> > Cheers
> > Peter
> > --
> > 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.
-- 
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] Protein-Ligand Interaction calculation

[Александр Лашков]

You can rebuild index file using gmx make_ndx gromacs util.
Alex

пн, 17 февр. 2020 г. в 15:19, Peter Mawanga :

> Hello everyone
>
> I used the CHARMM-GUI Membrane Builder to build a bilayer around my
> protein-ligand complex.
>
> However, unfortunately the ligand was not mentioned separately in the index
> (.ndx) file although it was mentioned in the topology (.top) file. Hence I
> am not able to calculate the energy between the protein and ligand using
> the energy (.edr) file.
>
> Please let me know if there is any workaround for this. It would be
> difficult to repeat the simulations again.
>
>
> --
> Cheers
> Peter
> --
> 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] Protein-Ligand Interaction calculation

[Peter Mawanga]

Hello everyone

I used the CHARMM-GUI Membrane Builder to build a bilayer around my
protein-ligand complex.

However, unfortunately the ligand was not mentioned separately in the index
(.ndx) file although it was mentioned in the topology (.top) file. Hence I
am not able to calculate the energy between the protein and ligand using
the energy (.edr) file.

Please let me know if there is any workaround for this. It would be
difficult to repeat the simulations again.


-- 
Cheers
Peter
-- 
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] Increase Graphene sheet size

[Mohamed Abdelaal]

Hello All,

I want to create a graphene sheet with a specific dimensions (10*15*0.284)
nm.

I created a .gro file as below ( as mentioned in this website
https://erastova.xyz/teaching/practical-simulations-for-molecules-and-materials/material-simulations/graphene-simulation-set-up/
)

GRM: 1 1 Rcc=1.420 Rhole=0.000 Center: Ring
4
1GRM   C1  1   0.061   0.071   0.000
1GRM   C2  2   0.184   0.142   0.000
1GRM   C3  3   0.184   0.284   0.000
1GRM   C4  4   0.061   0.355   0.000
0.2459510.4260000.284000

Now I don't know how to use genconf to repeat it until it gives me the
required dimensions. As using genconf -nbox will repeat the above into a
specific number of boxes but I can't get a sheet with accurate dimensions
of (10*15*0.284 nm).

I tried to generate a sheet using gencong and then use editconf to change
the dimensions to the required ones, but the problem is that using editconf
will put the graphene sheet in an empty box but will not change the
dimension as I want.

Another option is to divide the 10 (the required dimension) nm by 0.245951
(the dimension in the above .gro file) and to use the genconf with the
result but it will be a lot of decimals and I am not sure if it will also
give me the accurate dimension.

Can anybody help me or guide me how to solve that problem.

Thanks,
Mohamed
-- 
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] syntax error in GMXRC.csh in Gromacs2020

[Paul Bauer]

Hello,

Please open an issue on redmine for this.

Cheers

Paul

On Mon, 17 Feb 2020, 10:07 Harry Mark Greenblatt, <
harry.greenbl...@weizmann.ac.il> wrote:

> BS”D
>
> Seems that a bash formatted line has made it into the csh version of the
> GMXRC file:
>
> setenv GMXTOOLCHAINDIR=${GMXPREFIX}/share/cmake
>
> The “=“ should be a space.
>
> Harry
>
>
>
>
> 
> Harry M. Greenblatt
> Associate Staff Scientist
> Dept of Structural Biology   harry.greenbl...@weizmann.ac.il
> 
> Weizmann Institute of SciencePhone:  972-8-934-6340
> 234 Herzl St.Facsimile:   972-8-934-3361
> Rehovot, 7610001
> Israel
>
> --
> 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.

Re: [gmx-users] specified [ pairs ] and now get both LJ_SR and LJ_14 as energy output

[Alessandra Villa]

Hi,

I guess that the reported energy are averaged over the simulation time.
If you want to compare energies and understand what change in the topology
implied,
it is better to compare the energies of the first step using the same
starting structure.

The definition of LJ interactions (including 1-4 interaction) is not
trivial and involved different parameters,
I would suggest to check if your change in topology are doing what to
desire by looking at
http://manual.gromacs.org/documentation/current/reference-manual/topologies/topology-file-formats.html?highlight=pairs%20
with particular attention to values of gen-pairs, nrexcl, [pairs].

Best regards
Alessandra

On Thu, Feb 13, 2020 at 9:49 AM Luirink, R.A.  wrote:

> Anyone has advice/feedback?
>
> On 06/02/2020, 16:55, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> on behalf of Luirink, R.A." <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of
> r.a.luir...@vu.nl> wrote:
>
> Here some output to illustrate what I mean. This is what you would
> expect and what I also get for standard atom-atom interactions, not 1-4 and
> not specified in pairs. LJ-SR and Coul-SR but not LJ-14 and Coul-14
>
> Energy  Average   Err.Est.   RMSD  Tot-Drift
>
> ---
> Coul-SR:CXD-CDLAL 0.0134301 0.0035 0.00986618  0.0226416
> (kJ/mol)
> LJ-SR:CXD-CDLAL  -0.0871943  0.017  0.0466035  -0.109977
> (kJ/mol)
> Coul-14:CXD-CDLAL 0  0  0  0
> (kJ/mol)
> LJ-14:CXD-CDLAL   0  0  0  0
> (kJ/mol)
>
> This is what you would expect for 1-4 interactions (which I get for
> standard 1-4 interactions, but not the ones I specified) not LJ-SR and not
> Coul-SR but LJ-14 and Coul-14:
> Coul-SR:CXN-CDLAL 0  0  0  0
> (kJ/mol)
> LJ-SR:CXN-CDLAL   0  0  0  0
> (kJ/mol)
> Coul-14:CXN-CDLAL  0.7169660.00016  0.0100767
> -1.69012e-05  (kJ/mol)
> LJ-14:CXN-CDLAL   -0.2223597.1e-05 0.00496677
> -7.03428e-05  (kJ/mol)
>
> And this is what I get for my specified pairs BOTH LJ-SR and Coul-SR
> as LJ-14 and Coul-14:
> Coul-SR:CXZ-CXD0.674878   0.11   0.276414   0.758962
> (kJ/mol)
> LJ-SR:CXZ-CXD  0.373275   0.321.015532.06088
> (kJ/mol)
> Coul-14:CXZ-CXD 4.538610.20.468931.30594
> (kJ/mol)
> LJ-14:CXZ-CXD  0.186637   0.16   0.5077671.03044
> (kJ/mol)
>
> It seems like a bug to me, or I have overlooked something..
>
> On 06/02/2020, 14:44, "
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Luirink,
> R.A."  r.a.luir...@vu.nl> wrote:
>
> Gromacs version 2018.6 btw.
>
> On 06/02/2020, 13:54, "
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Luirink,
> R.A."  r.a.luir...@vu.nl> wrote:
>
> What I have tried is, instead of adding them to the [ pairs ]
> block, is change the epsilon value manually via the [ nonbon_params ]
> block. However, I can’t manually change the electrostatic interactions to
> account for the fudgeQQ (0.8333) for these specific pairs (or at least, I
> haven’t found a way to do so).
>
>
> From: "Luirink, R.A." 
> Date: Thursday, 6 February 2020 at 11:49
> To: "gmx-us...@gromacs.org" 
> Subject: specified [ pairs ] and now get both LJ_SR and LJ_14
> as energy output
>
> Hello,
> I try to specify a pair of atoms to be treated as a 1-4
> interaction (I replaced a covalent bond to a soft core restraint for free
> energy calculation purposes, and now gromacs does not recognize it anymore
> as 1-4 interaction, but it should still be treated as such).
> I added the pair to the [ pairs ] block in the topology. I did
> the same for 1-3 interactions, where I set the parameters to 0 for LJ
> interactions.
>
> When I check the energy between these pairs of atoms, I
> indeed get a value for LJ_14. However, my LJ_SR value is non-zero (and
> exactly twice the average value of LJ_14, where I have a fudge of 0.5). How
> can I fix this issue?
> Best,
> Rosa
> --
> 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
> 

[gmx-users] syntax error in GMXRC.csh in Gromacs2020

[Harry Mark Greenblatt]

BS”D

Seems that a bash formatted line has made it into the csh version of the GMXRC 
file:

setenv GMXTOOLCHAINDIR=${GMXPREFIX}/share/cmake

The “=“ should be a space.

Harry





Harry M. Greenblatt
Associate Staff Scientist
Dept of Structural Biology   
harry.greenbl...@weizmann.ac.il
Weizmann Institute of SciencePhone:  972-8-934-6340
234 Herzl St.Facsimile:   972-8-934-3361
Rehovot, 7610001
Israel

-- 
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] Cannot flush logfile - maybe you are out of disk space?

[Alessandra Villa]

Hi,

On Mon, Feb 17, 2020 at 7:48 AM Dilip.H.N  wrote:

> Dear all,
> I have extended a simulation (extension for 50 ns) and after some time i
> get the following error "Cannot flush logfile - maybe you are out of disk
> space?" and now the simulation has stopped running. The log file of the
> simulation is stopped at say 83ns-
>  Step   Time
> 4156600083132.0
>
> Now i have made the disk-free and still, the simulation is still struck. So
> now may i know how can i proceed..??
>
>
You can use the checkpoint file to re-start your simulation.
(see
http://manual.gromacs.org/documentation/current/onlinehelp/gmx-mdrun.html?highlight=gmx%20mdrun
)

If the old process is still active, better kill it.

Best regards
Alessandra



> Any suggestions are highly appreciated.
>
> Thank you.
> ---
> With Best Regards,
>
>
> *Dilip.H.N*
> Ph.D Student.
>
> [image: Mailtrack]
> <
> https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;
> >
> Sender
> notified by
> Mailtrack
> <
> https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;
> >
> 17/02/20,
> 12:14:16
> --
> 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.

Re: [gmx-users] Tabulated potentials

[Alessandra Villa]

Hi,
On Fri, Feb 14, 2020 at 5:17 PM Ali Khodayari <
ali.khoday...@student.kuleuven.be> wrote:

> Thank you Alessandra. However, fixing the topology did not remove the
> error. It still stands as before:
>
> A tabulated bond interaction table number 4 is out of the table range: r
> 0.575410, between table indices 575 and 576, table length 501
>
>
Where exactly did you get this error?

It looks like that your table is not covering all the request values (that
means that it is too short) or
the file is missing same values.

Best regards
Alessandra



> Anyone has any idea why it could be happening?
>
> My best,
> Ali
>
>
>
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> On Behalf Of
> Alessandra Villa
> Sent: donderdag 13 februari 2020 16:28
> To: gmx-us...@gromacs.org; gromacs.org_gmx-users <
> gromacs.org_gmx-users@maillist.sys.kth.se>
> Subject: Re: [gmx-users] Tabulated potentials
>
> Hi,
>
> On Wed, Feb 12, 2020 at 10:59 PM Ali Khodayari <
> ali.khoday...@student.kuleuven.be> wrote:
>
> > Dear Gromacs users,
> >
> > I’ve got a question regarding the tabulated potentials for bonded
> > interactions.
> >
> > Gromacs recognises and reads the non-bonded potential tables through
> > the energy groups specified. But how can I refer each bond type to its
> table?
> >
> > I have derived coarse-grained potentials for a cellobiose-water system.
> > There are 11 beads (4 bead types) in each cellobiose molecule, and
> > each water molecule is coarse-grained as one bead. Overall, there are
> > 3 bonded terms for 3 bond types, 3 anglular potentials for 3 angle
> > types, and 2 dihedral potential tables for two types of dihedrals. The
> > tables are named as table_b1.xvg, table_b2.xvg, and so on.
> >
> Now my question is, how does gromacs recognise which table is regarding
> > which bonded term? The simulation crashes at the very beginning giving
> > me the following error:
> >
> >
> In topol.top one specifies which table is used for which interaction
> (bond, angle, dihedral). See the table below for the synthases
>
>
> http://manual.gromacs.org/documentation/current/reference-manual/topologies/topology-file-formats.html#topology-file
>
> Best regards
> Alessandra
>
>
>
> > A tabulated bond interaction table number 1 is out of the table range:
> > r 0.511823, between table indices 511 and 512, table length 501
> >
> > I believe this is caused due to high forces on atoms indeed, but it
> > might be also because tables are not specified to the correct bond type.
> >
> >
> > Kind regards,
> > Ali
> > --
> > 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.
>
> --
> 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.