Re: [gmx-users] gromacs instillation

[Ali Ahmed]

Dear Rahul,
Thank you for your answer. Yes, I did remove the old version and all its
dependencies.
Usually, I use these commands for installation

mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
make
make check
sudo make install
source /usr/local/gromacs/bin/GMXRC

This time I got this error and tried several options with no luck


Thanks
Ali



On Wed, Apr 10, 2019 at 10:55 PM RAHUL SURESH 
wrote:

> Hi
>
> On Thu 11 Apr, 2019, 8:39 AM Ali Ahmed,  wrote:
>
> > Hello GMX users
> > I have installed gromacs 2019.1 on Ubuntu 16.04 and everything was well.
> > I run: source /usr/local/gromacs/bin/GMXRC and checked the version, it
> was
> > 2019.1.
> > When I open a new terminal and hit gmx, it says gromacs is currently not
> > installed.
>
> This means gromacs is not installed in the source directory. Simple., You
> will know where you have the gromacs executable. Just give that address in
> source. Or better set it in bash so you needn't go for source everytime.
>
> > You can install it by typing:  sudo apt install gromacs. When I
> > did it, the version became 5.1.2.
> >
>
> That's wrong procedure. If you want 2019 version then you got to start
> from scratch. Delete all you preexisting gromacs file and reinstall 2019
> Ver. Don't use apt-get.
>
> >
> > Any idea how to solve it!
> >
> > Thank you
> > Ali
> > --
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[gmx-users] Atom name mismatch between gro and top file

[RAHUL SURESH]

Hi Users.

While doing protein-ligand simulation, I get a warning which state
atom name mismatch between solv.gro and topol.top and name from top file be
considered and gro will be ignored. Yes, there is a mismatch, as in gro
file, the atom was in the order C-O-O and in itp file added to top, the
order was O-C-O. the itp file was generated by prodrg server.

1. Is it fine to ignore the warning and continue with the simualtion?

2. If not, which file should i  rename? gro or itp?


Thank you
-- 
*Regards,*
*Rahul *
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Re: [gmx-users] gromacs instillation

[RAHUL SURESH]

Hi

On Thu 11 Apr, 2019, 8:39 AM Ali Ahmed,  wrote:

> Hello GMX users
> I have installed gromacs 2019.1 on Ubuntu 16.04 and everything was well.
> I run: source /usr/local/gromacs/bin/GMXRC and checked the version, it was
> 2019.1.
> When I open a new terminal and hit gmx, it says gromacs is currently not
> installed.

This means gromacs is not installed in the source directory. Simple., You
will know where you have the gromacs executable. Just give that address in
source. Or better set it in bash so you needn't go for source everytime.

> You can install it by typing:  sudo apt install gromacs. When I
> did it, the version became 5.1.2.
>

That's wrong procedure. If you want 2019 version then you got to start
from scratch. Delete all you preexisting gromacs file and reinstall 2019
Ver. Don't use apt-get.

>
> Any idea how to solve it!
>
> Thank you
> Ali
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[gmx-users] gromacs instillation

[Ali Ahmed]

Hello GMX users
I have installed gromacs 2019.1 on Ubuntu 16.04 and everything was well.
I run: source /usr/local/gromacs/bin/GMXRC and checked the version, it was
2019.1.
When I open a new terminal and hit gmx, it says gromacs is currently not
installed. You can install it by typing:  sudo apt install gromacs. When I
did it, the version became 5.1.2.

Any idea how to solve it!

Thank you
Ali
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Re: [gmx-users] Different versions of gromacs

[Bratin Kumar Das]

Thanks

On Wed 10 Apr, 2019, 4:52 PM RAHUL SURESH  It won't work in lower version than 2016. I don't think it will have any
> problem with higher version and influence of the mdrun is not altered I
> guess as it is a factor of your mdp settings for higher versions
>
> On Wed 10 Apr, 2019, 3:41 PM Bratin Kumar Das, <
> 177cy500.bra...@nitk.edu.in>
> wrote:
>
> > Hi
> > Can I run equilibration simulation in one version (ex gromacs2016.5)
> > and production simulation in other version. Do the version have some
> > influence in simulation.
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Re: [gmx-users] disabling nonbonded interactions between two specific groups

[Dallas Warren]

I imagine you could do the first by having the two groups represented by
duplicated atom types (you'd have to create them in the FF files), then
turn off the interactions between them using normal lamba methods, but
leaving all the other interactions untouched.

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 Thu, 11 Apr 2019 at 08:33, Irem Altan  wrote:

> Hi all,
>
> Is it possible to disable nonbonded interactions between two specific
> groups? What I would like to do is a type of alchemical transformation to
> calculate free energies. Are  the following steps possible within Gromacs?
>
> - to have a molecule represented with standard force fields AND a Lennard
> Jones particle superimposed on it
> - the molecules interact with each other and the LJ particles interact
> with each other but the molecules don’t interact with LJ particles
> - across multiple simulations, the interaction energy of one species gets
> turned off gradually
>
> For the last part, is it possible to weaken the bonded interactions of the
> molecules and not have them fall apart by restraining the bond lengths with
> lincs? If so, can something similar be done to the dihedrals?
>
> Best,
> Irem
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[gmx-users] problems with pull code on Martini CG

[Bennett Addison]

Hello gromacs users,

I am fairly new to MD, trying hard to troubleshoot this issue myself before
posting. But I am at a loss.

I am trying to simulate pulling on a large protein, using Martini CG
simulations and adding the pull code. I am following tutorials for umbrella
sampling (all atom) and for martini protein simulations. Basically, the
exact same setup procedure works when the box size is small, but when I
scale up, things get screwy.

For example: 200 AA protein, placed 50 x 12 x 12 box and pull along X (see
pull code below: using direction-periodic geometry, pull along vector -1.0
0.0 0.0)

gmx editconf -f CG.pdb -o newbox.gro -box 50 12 12 -center 7 6 6

Followed by minimization in vac, solvate, minimize, equilibrate, then
create groups with gmx make_ndx, assign Chain_A as anchored residue, assign
Chain_B as residue to pull, make sure position restraints are correct, and
finally setup and run md_pull.mdp. This simulation works great. I see a
nice unfolding using martini CG model.
Pull code:

; Pull code

pull= yes

pull_ncoords= 1 ; only one reaction coordinate

pull_ngroups= 2 ; two groups defining one reaction
coordinate

pull_group1_name= Chain_A

pull_group2_name= Chain_B

pull_coord1_type= umbrella  ; harmonic potential

pull_coord1_geometry = direction-periodic ;

pull_coord1_vec = -1.0 0.0 0.0

pull_coord1_groups  = 1 2

pull_coord1_start   = yes   ; define initial COM distance > 0

pull_coord1_rate= 0.05  ; 0.05 nm per ps = 5 nm per ns

pull_coord1_k   = 1000  ; kJ mol^-1 nm^-2



Now when I try to replicate the exact same setup but using a larger box (100nm
20nm 20nm) everything fails. When I visualize the trajectory my protein
does not appear to be pulled, but the position output pullx.xvg shows
increase in distance, pullf.xvg shows no changes in force, and if I plot
distance between Chain_A and Chain_B using gmx distance, I see an expected
distance increase.


DOES NOT WORK: gmx editconf -f CG.pdb -o new box.gro -box 100 20 20 -center
8 10 10 (pullx looks ok, but pullf is flat, protein does not extend)

WORKS: gmx editconf -f CG.pdb -o new box.gro -box 50 12 12 -center 5 6 6
(trajectory looks great, pullf and pullx as expected)


Every other parameter / setup procedure is the same, just box size is
different. I need a larger box on my bigger protein (200 AAs) because it
will fully extend past 50nm.


I have tried with two configurations, same issues

- gromacs version 5.1.5 on a computing cluster, single node, AMD with 32
cores

- gromacs version 2018.3 on local machine with intel xeon E5 processors, 40
cores with GPU acceleration


Does anybody know why this may be happening, and how I can get around it?


Thank you!

-Bennett



Dr. Bennett Addison
Manager, SDSU NMR Facility
baddi...@sdsu.edu
206-235-5415  (cell)
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[gmx-users] disabling nonbonded interactions between two specific groups

[Irem Altan]

Hi all,

Is it possible to disable nonbonded interactions between two specific groups? 
What I would like to do is a type of alchemical transformation to calculate 
free energies. Are  the following steps possible within Gromacs?

- to have a molecule represented with standard force fields AND a Lennard Jones 
particle superimposed on it
- the molecules interact with each other and the LJ particles interact with 
each other but the molecules don’t interact with LJ particles
- across multiple simulations, the interaction energy of one species gets 
turned off gradually

For the last part, is it possible to weaken the bonded interactions of the 
molecules and not have them fall apart by restraining the bond lengths with 
lincs? If so, can something similar be done to the dihedrals?

Best,
Irem
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Re: [gmx-users] Surfactant from experiments to MD simulation

[André Farias de Moura]

Hi Alexander,

besides being really hard to achieve the um scale, the timescales also tend
to be too large for that kind of system, so direct atomistic modelling
might just be useless here even if you get the model drawn. The size of the
trajectory might easily become too large to be properly analyzed later.

in principle CG might help to achieve both a larger length scale and a
longer timescale, but I guess that you would be still far from the
experimental regime, so maybe it is not that helpful.

if the actual size and timescales cannot be properly reached then I would
go for simplified models depicting details of the actual system of
interest. For instance a periodic model system of your material with a few
nm in edge length could be used to study the adsorption patterns of the
surfactant. If the material has well-defined crystalline structure, then
different faces would have to be considered.

Although indirect, these simulations might provide evidence for the
stabilization mechanisms.

I hope it helps.

Andre

On Tue, Apr 9, 2019 at 11:53 PM Alex  wrote:

> Dear all,
> My question below is not directly a Gromacs's technical issue, so sorry for
> posting it here, however, any comment would be highly appreciated;
>
> A long surfactant (Molecular Weight (MW) of around 1200 g/mol) with weight
> fraction of 0.8 % in the system of emulsion works to keep the particle's
> size of a material around 1 micrometer (um) of diameter experimentally.
> To model such emulsion in all atoms MD simulation we can't go for the
> particles of 1 um diameter, but far less to a particle with around only 7
> nm of diameter. From 1 um particle in experiment to 7 nm one in MD
> simulation, the surface-volume of particle gets change, so that, using the
> surfactant with similar MW and weight fraction as the ones used in
> experiments does not work in MD simulations, so, would you please share
> your idea and though on how to mimic the MD simulations to experiments as
> mush as possible?
>
> Best regards,
> Alexander
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-- 
_

Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090
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Re: [gmx-users] WG: WG: Issue with CUDA and gromacs

[Szilárd Páll]

Hi,
On Wed, Apr 10, 2019 at 4:19 PM Tafelmeier, Stefanie <
stefanie.tafelme...@zae-bayern.de> wrote:

> Dear Szilárd and Jon,
>
> many thanks for your support.
>
> The system was Ubuntu 18.04 LTS, gcc 7.3 and CUDA 9.2.
> We upgraded now gcc (to 8.2) and CUDA (to 10.1).
>
> Now the regressiontests all pass.
> Also the tests Szilárd ask before are all running. Even just using mdrun
> -nt 80 works.
>

Great, this confirms that there was indeed a strange compatibility issue as
Jon suggested.

Many thanks! It seems that this was the origin of the problem.
>
> Just to be sure, I would like to have a look at the short range value of
> the complex test. As before some passed even without having the right
> values.
>

What do you mean by that?


> Is there a way to compare or a list with the correct outcome?
>

When the regressiontests are executed, the output by default lists all
commands that do the test runs as well as those that verify the outputs,
e.g.

$ perl gmxtest.pl complex
[...]
Testing acetonitrilRF . . . gmx grompp -f ./grompp.mdp -c ./conf -r ./conf
-p ./topol -maxwarn 10  >grompp.out 2>grompp.err
gmx check -s1 ./reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001
>checktpr.out 2>checktpr.err
 gmx mdrun-nb cpu   -notunepme >mdrun.out 2>&1
gmx check -e ./reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05
-lastener Potential >checkpot.out 2>checkpot.err
gmx check -f ./reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05
>checkforce.out 2>checkforce.err
PASSED but check mdp file differences

The gmx check commands do the checking and the the reference_s|d files to
comapre against.

--
Szilárd


> Anyway, here is the link to the tar-ball of the complex folder in case
> there is interest:
> https://it-service.zae-bayern.de/Team/index.php/s/mMyt3MPEfRrn8Ge
>
> Many thanks again for your help.
>
> Best wishes,
> Steffi
>
>
>
>
> -Ursprüngliche Nachricht-
> Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Im Auftrag von
> Jonathan Vincent
> Gesendet: Dienstag, 9. April 2019 22:13
> An: gmx-us...@gromacs.org
> Betreff: Re: [gmx-users] WG: WG: Issue with CUDA and gromacs
>
> Hi,
>
> Which operating system are you running on? We have seen some strange
> behavior with large number of threads, gcc 7.3 and a newish version of
> glibc. Specifically the default combination that comes with Ubuntu 18.04
> LTS, but it might be more generic than that.
>
> My suggestion would be to update to gcc 8.3 and CUDA 10.1 (which is
> required for CUDA support of gcc 8), which seemed to fix the problem in
> that case.
>
> If you still have problems we can look at this some more.
>
> Jon
>
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> On Behalf Of Szilárd
> Páll
> Sent: 09 April 2019 20:08
> To: Discussion list for GROMACS users 
> Subject: Re: [gmx-users] WG: WG: Issue with CUDA and gromacs
>
> Hi,
>
> One more test I realized it may be relevant considering that we had a
> similar report earlier this year on similar CPU hardware:
> can you please compile with -DGMX_SIMD=AVX2_256 and rerun the tests?
>
> --
> Szilárd
>
>
> On Tue, Apr 9, 2019 at 8:35 PM Szilárd Páll 
> wrote:
>
> > Dear Stefanie,
> >
> > On Fri, Apr 5, 2019 at 11:48 AM Tafelmeier, Stefanie <
> > stefanie.tafelme...@zae-bayern.de> wrote:
> >
> >> Hi Szilárd,
> >>
> >> thanks for your advices.
> >> I performed the tests.
> >> Both performed without errors.
> >>
> >
> > OK, that excludes simple and obvious issues.
> > Wild guess, but can you run those again, but this time prefix the
> > command with "taskset -c 22-32"
> > ? This makes the tests use cores 22-32 just to check if using a
> > specific set of cores may somehow trigger an error.
> >
> > What CUDA version did you use to compiler the memtest tool -- was it
> > the same (CUDA 9.2) as the one used for building GROMACS?
> >
> > Just to get it right; I have to ask in more detail, because the
> > connection
> >> between is the CPU/GPU and calculation distribution is still a bit
> >> blurry to me:
> >>
> >> If the output of the regressiontests show that the test crashes after
> >> 1-2 steps, this means there is an issue between the transfer between
> >> the CPU and GPU?
> >> As far as I got the short range calculation part is normally split
> >> into nonbonded -> GPU and bonded -> CPU?
> >>
> >
> > The -nb/-pme/-bonded flags control which tasks executes where (if not
> > specified defaults control this); the output contains a report which
> > summarizes where the major force tasks are executed, e.g. this is from
> > one of your log files which tells that PP (i.e. particle tasks like
> > short-range
> > nonbonded) and the full PME tasks are offloaded to a GPU with ID 0
> > (and to check which GPU is that you can look at the "Hardware
> > detection" section of the log):
> >
> > 1 GPU selected for this run.
> > Mapping of GPU IDs to the 2 

[gmx-users] Tpr version check

[Erik Marklund]

Hi users,

I accidentally used an older version (2016.3) to run trjconv on some 
trajectories. Some conversions worked, seemingly depending on pbc options etc, 
whereas others stopped with the following output:

Back Off! I just backed up mol.xtc to ./#mol.xtc.1#
 ->  frame  0 time0.000
---
Program: gmx trjconv, version 2016.3
Source file: src/gromacs/pbcutil/pbc.cpp (line 94)

Fatal error:
Unknown ePBC=1051770189 in ePBC2npbcdim

Call me a hopeless nostalgic, but I remember a time when such mistakes rendered 
an error saying that I am using an older version of gmx than the version used 
to generate the tpr file. Is that not a thing anymore, and this is the expected 
behaviour? Seems problematic if gmx tools try to read nonsense data (from the 
viewpoint of the gromacs version used).

Kind regards,
Erik
__
Erik Marklund, PhD, Associate Professor of Biochemistry
Associate Senior Lecturer in Computational Biochemistry
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4562
erik.markl...@kemi.uu.se









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[gmx-users] Energy from a subgroup of molecules

[p buscemi]

Dear Users,
I've performed an adsorption experiment in which a fraction of molecules in 
solution adsorb to a surface. I can extract the index of those adsorbed, and I 
can obtain the total interaction ( LJ ) of the energy group with the surface.
I can estimate the average interaction of the adsorbed molecules by dividing 
the total energy by the number of molecules within a certain distance ( the 
index number )
How might I use gmx energy to recalculate the interaction using the original 
surface but only the adsorbed molecules specified in the index file... 
something like
"gmx energy -f starting.gro -n index.ndx"

A single point calculation would be quite satisfactory.
thanks
Paul
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Re: [gmx-users] WG: WG: Issue with CUDA and gromacs

[Tafelmeier, Stefanie]

Dear Szilárd and Jon,

many thanks for your support.

The system was Ubuntu 18.04 LTS, gcc 7.3 and CUDA 9.2.
We upgraded now gcc (to 8.2) and CUDA (to 10.1). 

Now the regressiontests all pass.
Also the tests Szilárd ask before are all running. Even just using mdrun -nt 80 
works.

Many thanks! It seems that this was the origin of the problem.

Just to be sure, I would like to have a look at the short range value of the 
complex test. As before some passed even without having the right values.
Is there a way to compare or a list with the correct outcome?
Anyway, here is the link to the tar-ball of the complex folder in case there is 
interest:   
https://it-service.zae-bayern.de/Team/index.php/s/mMyt3MPEfRrn8Ge 

Many thanks again for your help.

Best wishes,
Steffi 




-Ursprüngliche Nachricht-
Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Im Auftrag von 
Jonathan Vincent
Gesendet: Dienstag, 9. April 2019 22:13
An: gmx-us...@gromacs.org
Betreff: Re: [gmx-users] WG: WG: Issue with CUDA and gromacs

Hi,

Which operating system are you running on? We have seen some strange behavior 
with large number of threads, gcc 7.3 and a newish version of glibc. 
Specifically the default combination that comes with Ubuntu 18.04 LTS, but it 
might be more generic than that. 

My suggestion would be to update to gcc 8.3 and CUDA 10.1 (which is required 
for CUDA support of gcc 8), which seemed to fix the problem in that case.

If you still have problems we can look at this some more.

Jon

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 On Behalf Of Szilárd Páll
Sent: 09 April 2019 20:08
To: Discussion list for GROMACS users 
Subject: Re: [gmx-users] WG: WG: Issue with CUDA and gromacs

Hi,

One more test I realized it may be relevant considering that we had a similar 
report earlier this year on similar CPU hardware:
can you please compile with -DGMX_SIMD=AVX2_256 and rerun the tests?

--
Szilárd


On Tue, Apr 9, 2019 at 8:35 PM Szilárd Páll  wrote:

> Dear Stefanie,
>
> On Fri, Apr 5, 2019 at 11:48 AM Tafelmeier, Stefanie < 
> stefanie.tafelme...@zae-bayern.de> wrote:
>
>> Hi Szilárd,
>>
>> thanks for your advices.
>> I performed the tests.
>> Both performed without errors.
>>
>
> OK, that excludes simple and obvious issues.
> Wild guess, but can you run those again, but this time prefix the 
> command with "taskset -c 22-32"
> ? This makes the tests use cores 22-32 just to check if using a 
> specific set of cores may somehow trigger an error.
>
> What CUDA version did you use to compiler the memtest tool -- was it 
> the same (CUDA 9.2) as the one used for building GROMACS?
>
> Just to get it right; I have to ask in more detail, because the 
> connection
>> between is the CPU/GPU and calculation distribution is still a bit 
>> blurry to me:
>>
>> If the output of the regressiontests show that the test crashes after 
>> 1-2 steps, this means there is an issue between the transfer between 
>> the CPU and GPU?
>> As far as I got the short range calculation part is normally split 
>> into nonbonded -> GPU and bonded -> CPU?
>>
>
> The -nb/-pme/-bonded flags control which tasks executes where (if not 
> specified defaults control this); the output contains a report which 
> summarizes where the major force tasks are executed, e.g. this is from 
> one of your log files which tells that PP (i.e. particle tasks like 
> short-range
> nonbonded) and the full PME tasks are offloaded to a GPU with ID 0 
> (and to check which GPU is that you can look at the "Hardware 
> detection" section of the log):
>
> 1 GPU selected for this run.
> Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node:
>   PP:0,PME:0
> PP tasks will do (non-perturbed) short-ranged interactions on the GPU 
> PME tasks will do all aspects on the GPU
>
> For more details, please see
> http://manual.gromacs.org/documentation/2019.1/user-guide/mdrun-perfor
> mance.html#running-mdrun-with-gpus
>
> We have seen two types of errors so far:
> - "Asynchronous H2D copy failed: invalid argument" which is still 
> mysterious to me and has showed up both in your repeated manual runs 
> as well as the regressiontest; as this aborts the run
> - Failing regressiontests with either invalid results or crashes 
> (below above abort): to be honest I do not know what causes these but 
> given that results
>
> The latter errors indicate incorrect results, in your last "complex" 
> tests tarball I saw some tests failing with LINCS errors (and 
> indicating NaN
> values) and a good fraction of tests failing with a GPU-side 
> assertions -- both of which suggest that things do go wrong on the GPU.
>
> And does this mean that maybe also the calculation I do, have wrong
>> energies? Can I trust my results?
>>
>
> At this point I can unfortunately not recommend running production 
> simulations on this machine.
>
> Will try to continue exploring the possible 

[gmx-users] Polymerization in gromacs

[이영규]

Dear users,

I am currently having trouble with polymerization, joining the nearby atoms
if they are within the polymerization distance. My system consists of 2
monomers. The procedure what I did was that first put monomers in the box
and equilibrate it by extending box size. After I get the final box size
and equilibrate the system, I have to connect monomers. This point is what
I am stuck and here's my question.

Q. Is there any command or procedure that I can do with gromacs about the
polymerization? If not, does anyone let me know how to do or the software
doing this polymerization?

Thanks in advance
-- 

Yeongkyu Lee

M.S student

Department of Physics

501, Jinjudaero, Jinju, Gyeongnam
,
52828, Korea

Email: monsterpl...@gmail.com

Phone: +82-10-8771-2190
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[gmx-users] Contact autocorrelation function in Gromacs

[Mahsa]

Dear all,

I want to calculate the contact duration of ions with special atoms in
polymer chains within 3 Å of the ion.
I found gmx hbond as a good option for this analysis, but I have some
questions regarding this calculation. By the way, the version of gromacs is
2018.3.
1.  I used the following command:
gmx  hbond -s topol.tpr -f md.xtc -n index_contact.ndx -contact -r 0.3 -num
contact.xvg -g contact.log -ac contact_ac.xvg
in the gromacs manual it is not clear whether r or r2 should be used for
this analysis. I tried this as well:
gmx  hbond -s topol.tpr -f md.xtc -n index_contact.ndx -contact -r2 0.3
-num contact.xvg -g contact.log -ac contact_ac.xvg
The final results were little bit different from the first one. Which one
is correct -r or -r2?
2. At the end of this calculation, I get the following warning:
WARNING: Correlation function is probably not long enough
because the standard deviation in the tail of C(t) > 0.001

I used the trajectory of 500 ns simulation time but still get this warning.
I also tried trajectory with saving every frame but still get the warning.
How can I solve this?
3. The tail of ACF goes to negative values, I found this link for the
similar question:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2011-June/062181.html
Does this means that I should consider the second column of y values in the
contac_ac.xvg file instead of the first one?

Best regards,
Mahsa
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Re: [gmx-users] Different versions of gromacs

[RAHUL SURESH]

It won't work in lower version than 2016. I don't think it will have any
problem with higher version and influence of the mdrun is not altered I
guess as it is a factor of your mdp settings for higher versions

On Wed 10 Apr, 2019, 3:41 PM Bratin Kumar Das, <177cy500.bra...@nitk.edu.in>
wrote:

> Hi
> Can I run equilibration simulation in one version (ex gromacs2016.5)
> and production simulation in other version. Do the version have some
> influence in simulation.
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[gmx-users] Different versions of gromacs

[Bratin Kumar Das]

Hi
Can I run equilibration simulation in one version (ex gromacs2016.5)
and production simulation in other version. Do the version have some
influence in simulation.
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[gmx-users] atom types of hydrogens

[boshra.moradi.61]

 Dear all, 

i'm new om gromacs and my molecule is D-glucosamine.i introduced it via
inserting in aminoacids.rtp file.my question is how nominate four
H-atoms . i want atomtypes.atp to find the atometype of these four atoms
but i didn't find.i want you to guide me about this problem,could you-- 
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[gmx-users] Topology errors: covalent bonds across periodic boundaries

[Rachel Baarda]

Dear Gromacs users,

I am trying to simulate an "infinite" protein chain by covalently bonding
the last residue of my structure to the first residue across the periodic
boundary. I have modified the topology file to include these bonded
interactions and have specified "periodic-molecules=yes" in my mdp file.
However, when attempting to use grompp, I get many errors of the type "No
default Bond types" "No default U-B types" etc.

Below is a snippet of the first residue of my structure:
0ALA  N1  -2.130  11.857   5.885
0ALA HN2  -2.194  11.930   5.907
0ALA CA3  -2.193  11.725   5.916

And a snippet of the last residue:
  179THR   HG23 2660   3.379  11.851   6.387
  179THR  C 2661   3.583  11.711   6.162
  179THR  O 2662   3.514  11.783   6.087

I have identified and added ~30 bonded interactions to my topology file.
For example, the carbon in THR should be bonded to the nitrogen in ALA, so
I have added the following line (line #5541 in my .top file):
[ bonds ]
;  aiaj functc0c1c2c3
2661 1 1

However, grompp returns the following error:
ERROR 1 [file monomer_3.top, line 5541]:
  No default Bond types

Similar errors are produced for most (but not all) of the added
interactions. All of the "pairs" and four of the "dihedrals" were processed
without errors. I cannot find a pattern in the dysfunctional vs functional
lines. For example, the following dihedral did not return an error:
(179THR  N 2649   )-(179THR CA 2651   )-(179THR  C 2661
)-(0ALA  N1  )
However, this dihedral did:
(179THR CA 2651   )-(179THR  C 2661   )-(0ALA  N1  )-(0ALA
   HN2  )

Any help in debugging this would be much appreciated!

Thanks in advance,

Rachel Baarda
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[gmx-users] Protein dipole moments

[Emran Heshmati]

What are the physical meaning of <|M|^2> and <|M|>^2 in the outputs of gmx
dipoles command ?? Any help is welcome.
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