Re: [gmx-users] Check the 1-4 interactions, and the non-bonded pairs in the output

[Alessandra Villa]

Hi

On Thu, Dec 5, 2019 at 7:01 PM Suvardhan Jonnalagadda <
j.su.vard...@gmail.com> wrote:

> Hi all,
>
> I have performed NPT simulation in GROMACS 5.4.1. In the 'forcefield.itp'
> file I have mentioned 'gen-pairs' as 'yes', and also the 'Fudge-LJ' was
> specified. From the output I want to check and confirm the LJ parameters of
> 1-4, and non-bonded pairs. How do I check it?
>

gmx dump -s topol.tpr  reads tpr file  and prints that to standard
output in a readable format.

If you are implementing an existing force field you could check that the
values of
all the potential energy terms are  the one excepted for that geometry (e.i
obtained from another source)

Best regards
Alessandra




> Thank you,
>
> Best regards,
> Vardhan
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[gmx-users] How to calculate potential energy with dynamics selection index?

[Peiyin Lee]

Dear users,

   I am trying to calculate the VDW potential energy and electrostatic
energy for solvent in the first solvation shell and in bulk for my
simulation systems. In order to calculate the potential for solvent in the
FSS, I have to do gmx_energy with dynamics selection and do a rerun.
However, gmx_make_ndx only supports static selection. I have also tried
gmx_select, but this command gave me selections like "xx within 0.5 of yy"
for every frame and produced a massive amounts of indexes. Each index seems
to be treated as static index when I did a rerun and calculated gmx_energy,
which is not what I expected. Does anyone know any way to perform
dynamics selection? Thank you in advance!


Regards,
Peiyin
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Re: [gmx-users] The total charge is not integer : -0.00465

[SAKO MIRZAIE]

Dear Justin,

Thank you for your answer. when I use just one chain of polymer with the
protein, the charge is an integer but when I employ "insert molecules" to
add more than one polymer chain, the charge will not be an integer. I am
wondering what's the problem?

Best regards

On Tue, Dec 3, 2019 at 4:04 PM Justin Lemkul  wrote:

>
>
> On 12/3/19 3:59 PM, SAKO MIRZAIE wrote:
> > Hi All,
> > I did some MD  studies on a protein: polymer system. After running
> grompp,
> > it said, "the total charge is not an integer". the total charge is
> -0.00465.
> > Can I continue the MD by adding -maxwarn flag? or it will be a problem
> and
> > I will get unrealistic results?
>
> In general, it is never a good idea to use -maxwarn.
>
> The magnitude of that total charge is suspiciously high and you should
> check your topology for proper charge assignment.
>
> -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
>
> ==
>
>

-- 
***
Sako Mirzaie
Sako Mirzaie
Ph.D. in biochemistry, Assistant Professor, Science Faculty, Islamic Azad
University of Sanandaj, Sanandaj, Iran

Visiting Professor, Advanced Pharmaceutics

& Drug Delivery Laboratory

Leslie Dan Faculty of Pharmacy

University of Toronto

144 College Street, Toronto, Ontario

Canada M5S 3M2

http://scholar.google.com/citations?user=viwZvVAJ&hl=en

http://www.scopus.com/authid/detail.url?authorId=54886431500

http://www.ncbi.nlm.nih.gov/pubmed/?term=sako+mirzaie
https://www.researchgate.net/profile/Sako_Mirzaie/publications/
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[gmx-users] Center of mass motion removal

[Alex]

Hi all,

I have a droplet containing two molecules types of A and B in water.
Unfortunately, I forgot to use the comm-grps = AB flag in my mdp file of
simulations so, the whole droplet just drifting around inside water. Now at
this point, I wonder if there is a tool in gromacs to remove the center of
mass motion of the whole trajectory?

I have already applied the
gmx trjconv -pbc mol
Then
gmx trjconv -pbc cluster -center yes

However, as I knew, they can not stop the COM motion.

Thank you
Alex
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Re: [gmx-users] Seg Fault with Gromacs gmx grompp command - Intel compiler

[Glenn (Gedaliah) Wolosh]

Thanks for the quick response. I do have the environment properly prepare via 
modules.

GW 


> On Dec 5, 2019, at 3:24 PM, Mark Abraham  wrote:
> 
> Hi,
> 
> I suspect you need to prepare the intel environment at run time like you
> did before compilation. Probably you (or a module you loaded) source-d a
> compilervars.sh file, and that's probably what you need here.
> 
> Mark
> 
> On Thu, 5 Dec 2019 at 20:22, Glenn (Gedaliah) Wolosh  >
> wrote:
> 
>> 
>> Also posted on the intel forum:
>> 
>> This problem is consistent with the following gromacs/compiler versions:
>> 
>> Gromacs 2019.4/Intel Parallel Studio 2019.4
>> 
>> Gromacs 2019.4/Intel 2017.2
>> 
>> Gromacs 2018.2/Intel Parallel Studio 2019.4
>> 
>> Gromacs 2018.5/Intel Parallel Studio 2019.4
>> 
>> The command to build and install gromacs in all cases is
>> 
>> export CC=icc
>> export CXX=icpc
>> export FC=ifort
>> 
>> cmake ..  -DGMX_FFT_LIBRARY=mkl \
>>  -DCMAKE_INSTALL_PREFIX=$HOME/sw/gromacs/intel/
>> &&  make VERBOSE=1 && make install
>> 
>> The gcc version in the PATH is 5.4.0
>> 
>> The OS is:
>> 
>> Scientific Linux release 6.10 (Carbon)
>> 
>> I am running the lysozyme tutorial:
>> http://www.mdtutorials.com/gmx/lysozyme/ <
>> http://www.mdtutorials.com/gmx/lysozyme/ 
>> >
>> The command that seg faults is
>> 
>> gmx grompp -f ions.mdp -c 1AKI_solv.gro -p topol.top -o ions.tpr -maxwarn 2
>> 
>> The gmx grompp command succeeds when using a version of gromacs compiled
>> with GCC
>> 
>> Any help would be greatly appreciated.
>> 
>> 
>> GW
>> --
>> Gromacs Users mailing list
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>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List 
>>  before
>> posting!
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>>  or
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>> .
>> 
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Re: [gmx-users] Problem restarting job 2016.4 with gromacs 2019-4

[Mark Abraham]

Hi,

A checkpoint restart is indeed not supported. But you can be creative with
the old version of gromacs e.g. gmx grompp -f -p -c -cpi old.cpt -s
new.tpr, and then that .tpr file has the content of the .cpt in a format
that the newer gmx will be able to run (unless we actually removed
necessary functionality)

Mark

On Wed, 4 Dec 2019 at 18:58, Justin Lemkul  wrote:

>
>
> On 12/4/19 11:58 AM, CROUZY Serge 119222 wrote:
> > Dear Gromacs users
> >
> > We just installed Gromacs 2019.4
> > And I get an error restarting free energy jobs (pull) run with Gromacs
> 2016.4
> > I' m using one GPU
> >gmx mdrun -nt 20 -s umbrella3_60ns.tpr -cpi umbrella3.cpt -deffnm
> umbrella3 -pf pullf-umbrella3.xvg -px pullx-umbrella3.xvg
> >
> > GROMACS version:2019.4
> > Precision:  single
> > Memory model:   64 bit
> > MPI library:thread_mpi
> > OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
> > GPU support:CUDA
> > SIMD instructions:  AVX2_256
> >
> > Using 1 MPI thread
> > Using 20 OpenMP threads
> > 1 GPU selected for this run.
> >
> > Fatal error:
> > Mismatch between number of energies in run input (52) and checkpoint
> file (51
> > or 51).
> >
> > And of course the run restarts OK with Gromacs 2016.4 ??
> > Anybody got an idea or bug fix ?
>
> It is not possible to continue your simulations with these different
> versions because of changes in what is saved to the checkpoint files. In
> general, you should not change major versions mid-simulation/mid-project
> because file formats change (and potentially due to changes in how the
> code works entirely!).
>
> -Justin
>
> >
> > Regards
> > Serge Crouzy
> >
>
> --
> ==
>
> 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] Seg Fault with Gromacs gmx grompp command - Intel compiler

[Mark Abraham]

Hi,

I suspect you need to prepare the intel environment at run time like you
did before compilation. Probably you (or a module you loaded) source-d a
compilervars.sh file, and that's probably what you need here.

Mark

On Thu, 5 Dec 2019 at 20:22, Glenn (Gedaliah) Wolosh 
wrote:

>
> Also posted on the intel forum:
>
> This problem is consistent with the following gromacs/compiler versions:
>
> Gromacs 2019.4/Intel Parallel Studio 2019.4
>
> Gromacs 2019.4/Intel 2017.2
>
> Gromacs 2018.2/Intel Parallel Studio 2019.4
>
> Gromacs 2018.5/Intel Parallel Studio 2019.4
>
> The command to build and install gromacs in all cases is
>
> export CC=icc
> export CXX=icpc
> export FC=ifort
>
> cmake ..  -DGMX_FFT_LIBRARY=mkl \
>   -DCMAKE_INSTALL_PREFIX=$HOME/sw/gromacs/intel/
> &&  make VERBOSE=1 && make install
>
> The gcc version in the PATH is 5.4.0
>
> The OS is:
>
> Scientific Linux release 6.10 (Carbon)
>
> I am running the lysozyme tutorial:
> http://www.mdtutorials.com/gmx/lysozyme/ <
> http://www.mdtutorials.com/gmx/lysozyme/>
> The command that seg faults is
>
> gmx grompp -f ions.mdp -c 1AKI_solv.gro -p topol.top -o ions.tpr -maxwarn 2
>
> The gmx grompp command succeeds when using a version of gromacs compiled
> with GCC
>
> Any help would be greatly appreciated.
>
>
> GW
> --
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[gmx-users] Seg Fault with Gromacs gmx grompp command - Intel compiler

[Glenn (Gedaliah) Wolosh]

Also posted on the intel forum:

This problem is consistent with the following gromacs/compiler versions:

Gromacs 2019.4/Intel Parallel Studio 2019.4

Gromacs 2019.4/Intel 2017.2

Gromacs 2018.2/Intel Parallel Studio 2019.4

Gromacs 2018.5/Intel Parallel Studio 2019.4

The command to build and install gromacs in all cases is

export CC=icc
export CXX=icpc
export FC=ifort

cmake ..  -DGMX_FFT_LIBRARY=mkl \
  -DCMAKE_INSTALL_PREFIX=$HOME/sw/gromacs/intel/  &&  
make VERBOSE=1 && make install

The gcc version in the PATH is 5.4.0

The OS is:

Scientific Linux release 6.10 (Carbon)

I am running the lysozyme tutorial: http://www.mdtutorials.com/gmx/lysozyme/ 

The command that seg faults is 

gmx grompp -f ions.mdp -c 1AKI_solv.gro -p topol.top -o ions.tpr -maxwarn 2

The gmx grompp command succeeds when using a version of gromacs compiled with 
GCC 

Any help would be greatly appreciated.


GW
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[gmx-users] Check the 1-4 interactions, and the non-bonded pairs in the output

[Suvardhan Jonnalagadda]

Hi all,

I have performed NPT simulation in GROMACS 5.4.1. In the 'forcefield.itp'
file I have mentioned 'gen-pairs' as 'yes', and also the 'Fudge-LJ' was
specified. From the output I want to check and confirm the LJ parameters of
1-4, and non-bonded pairs. How do I check it?

Thank you,

Best regards,
Vardhan
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Re: [gmx-users] run MD in vacuum

[dgfd dgdfg]

This settings work, but version isn't newest.

integrator<>=<->md
dt<><-->=<->0.001
nsteps<><-->=<->1010
nstxout><-->=<->1
nstcalcenergy<->=<->100
nstenergy<->=<->100

cutoff-scheme<->=<->group
pbc<--->=<->no
nstlist>=<->0
rlist<->=<->0
ns_type>=<->simple
coulomb-modifier<-->=<->none
vdw-modifier<-->=<->none
rcoulomb<-->=<->0
rvdw<-->=<->0

Tcoupl<><-->=<->V-rescale
tau-t<-><-->=<->0.1
tc-grps><-->=<->system
ref-t<-><-->=<->298.15

Pcoupl<><-->=<->no
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Re: [gmx-users] run MD in vacuum

[Justin Lemkul]

On 12/5/19 8:59 AM, HERNANDEZ ALBA Oscar (ECPM) wrote:

Hello Justin,

  


 I am starting using gromacs and I am still discovering all
the different possibilities that this software offers. However, I want to
run MD in vacuum, not in solution. I read that the newest versions of
gromacs (from 2019) allows to perform molecular dynamics in vacuum with
Verlet integration. However when I run the calculations with the vacuum
conditions (rlist, rcoulom, and rvdw = 0, and pbc=no), I get an error
message suggesting that I have to put a cut-off for all these non-bonded
interactions, along with the activation of periodic boundary conditions.
Is there any way to perform MD in vacuum with Verlet integration? If this
is the case, please could you send me the specific conditions that I have
to specify in the mdp file to run it properly?

  


I have no experience with running vacuum calculations in the latest 
version. Hopefully someone else on the list can help.


-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] run MD in vacuum

[HERNANDEZ ALBA Oscar (ECPM)]

Hello Justin,

 

I am starting using gromacs and I am still discovering all
the different possibilities that this software offers. However, I want to
run MD in vacuum, not in solution. I read that the newest versions of
gromacs (from 2019) allows to perform molecular dynamics in vacuum with
Verlet integration. However when I run the calculations with the vacuum
conditions (rlist, rcoulom, and rvdw = 0, and pbc=no), I get an error
message suggesting that I have to put a cut-off for all these non-bonded
interactions, along with the activation of periodic boundary conditions.
Is there any way to perform MD in vacuum with Verlet integration? If this
is the case, please could you send me the specific conditions that I have
to specify in the mdp file to run it properly? 

 

Thank you very much for your help

 

Oscar Hernandez Alba

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Re: [gmx-users] Gromacs 2019.4 - cudaStreamSynchronize failed issue

[Szilárd Páll]

Can you please file an issue on redmine.gromacs.org and attach the inputs
that reproduce the behavior described?

--
Szilárd

On Wed, Dec 4, 2019, 21:35 Chenou Zhang  wrote:

> We did test that.
> Our cluster has total 11 GPU nodes and I ran 20 tests over all of them. 7
> out of the 20 tests did have the potential energy jump issue and they were
> running on 5 different nodes.
> So I tend to believe this issue happens on any of those nodes.
>
> On Wed, Dec 4, 2019 at 1:14 PM Szilárd Páll 
> wrote:
>
> > The fact that you are observing errors alo the energies to be off by so
> > much and that it reproduces with multiple inputs suggest that this may
> not
> > a code issue. Did you do all runs that failed on the same hardware? Have
> > you excluded the option that one of those GeForce cards may be flaky?
> >
> > --
> > Szilárd
> >
> >
> > On Wed, Dec 4, 2019 at 7:47 PM Chenou Zhang  wrote:
> >
> > > We tried the same gmx settings in 2019.4 with different protein
> systems.
> > > And we got the same weird potential energy jump  within 1000 steps.
> > >
> > > ```
> > >
> > > Step   Time
> > >   00.0
> > >  Energies (kJ/mol)
> > >BondU-BProper Dih.  Improper Dih.  CMAP
> > Dih.
> > > 2.08204e+049.92358e+046.53063e+041.06706e+03
> >  -2.75672e+02
> > >   LJ-14 Coulomb-14LJ (SR)   Coulomb (SR)   Coul.
> > recip.
> > > 1.50031e+04   -4.86857e+043.10386e+04   -1.09745e+06
> > 4.81832e+03
> > >   PotentialKinetic En.   Total Energy  Conserved En.
> > Temperature
> > >-9.09123e+052.80635e+05   -6.28487e+05   -6.28428e+05
> > 3.04667e+02
> > >  Pressure (bar)   Constr. rmsd
> > >-1.56013e+003.60634e-06
> > >
> > > DD  step 999 load imb.: force 14.6%  pme mesh/force 0.581
> > >Step   Time
> > >10002.0
> > >
> > > Energies (kJ/mol)
> > >BondU-BProper Dih.  Improper Dih.  CMAP
> > Dih.
> > > 2.04425e+049.92768e+046.52873e+041.02016e+03
> >  -2.45851e+02
> > >   LJ-14 Coulomb-14LJ (SR)   Coulomb (SR)   Coul.
> > recip.
> > > 1.49863e+04   -4.91092e+043.10572e+04   -1.09508e+06
> > 4.97942e+03
> > >   PotentialKinetic En.   Total Energy  Conserved En.
> > Temperature
> > > 1.35726e+352.77598e+051.35726e+351.35726e+35
> > 3.01370e+02
> > >  Pressure (bar)   Constr. rmsd
> > >-7.55250e+013.63239e-06
> > >
> > >  DD  step 1999 load imb.: force 16.1%  pme mesh/force 0.598
> > >Step   Time
> > >20004.0
> > >
> > > Energies (kJ/mol)
> > >BondU-BProper Dih.  Improper Dih.  CMAP
> > Dih.
> > > 1.99521e+049.97482e+046.49595e+041.00798e+03
> >  -2.42567e+02
> > >   LJ-14 Coulomb-14LJ (SR)   Coulomb (SR)   Coul.
> > recip.
> > > 1.50156e+04   -4.85324e+043.01944e+04   -1.09620e+06
> > 4.82958e+03
> > >   PotentialKinetic En.   Total Energy  Conserved En.
> > Temperature
> > > 1.35726e+352.79206e+051.35726e+351.35726e+35
> > 3.03115e+02
> > >  Pressure (bar)   Constr. rmsd
> > >-5.50508e+013.64353e-06
> > >
> > > DD  step 2999 load imb.: force 16.6%  pme mesh/force 0.602
> > >Step   Time
> > >30006.0
> > >
> > >
> > > Energies (kJ/mol)
> > >BondU-BProper Dih.  Improper Dih.  CMAP
> > Dih.
> > > 1.98590e+049.88100e+046.50934e+041.07048e+03
> >  -2.38831e+02
> > >   LJ-14 Coulomb-14LJ (SR)   Coulomb (SR)   Coul.
> > recip.
> > > 1.49609e+04   -4.93079e+043.12273e+04   -1.09582e+06
> > 4.83209e+03
> > >   PotentialKinetic En.   Total Energy  Conserved En.
> > Temperature
> > > 1.35726e+352.79438e+051.35726e+351.35726e+35
> > 3.03367e+02
> > >  Pressure (bar)   Constr. rmsd
> > > 7.62438e+013.61574e-06
> > >
> > > ```
> > >
> > > On Mon, Dec 2, 2019 at 2:13 PM Mark Abraham 
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > What driver version is reported in the respective log files? Does the
> > > error
> > > > persist if mdrun -notunepme is used?
> > > >
> > > > Mark
> > > >
> > > > On Mon., 2 Dec. 2019, 21:18 Chenou Zhang,  wrote:
> > > >
> > > > > Hi Gromacs developers,
> > > > >
> > > > > I'm currently running gromacs 2019.4 on our university's HPC
> cluster.
> > > To
> > > > > fully utilize the GPU nodes, I followed notes on
> > > > >
> > > > >
> > > >
> > >
> >
> http://manual.gromacs.org/documentation/current/user-guide/mdrun-performance.html
> > > > > .
> > > > >
> > > > >
> > > > > And here is the command I used for my runs.
> > > > > ```
> > > > > gmx mdrun -v -s $TPR -deffnm md_seed_fixed -ntmpi 8 -pin on -nb gpu
> > > > -ntomp
> > > > > 3 -pme gpu -pmefft gpu -npme 1 -gputasks 00112233 -maxh $HOURS -cpt
> > 60
> > > > -cpi
> > > > > -noappend
> > > > > `

Re: [gmx-users] Potential or total energy in dhdl files

[Alessandra Villa]

Hi,

On Wed, Dec 4, 2019 at 11:39 AM Александр Лашков 
wrote:

> Thank you for anwer, but i don't understand this. For BAR this terms not
> necessary. But for MBAR i'am not sure. In third party program - alchemlyb
> and alchemystry-analysis, total energy or potential used for calculate
> reduced potential if this terms include in dhdl files.
> Sincerely,
>

I am not familiar with these third party programs.  If those programs read
as input  dhdl.xvg file and
they require the values of total and potential energy to be written in the
dhdl.xvg.
Then you can activate the option in mdp according to which information the
program requires to have in the dhdl file.

Potential and total energy in GROMACS are generally stored in edr file and
written log file, the mdp option  "dhdl-print-energy" gives an extra option
to have those values written in the dhdl.xvg file.

Best regards
Alessandra





> Alexander
>
> ср, 4 дек. 2019 г. в 12:02, Alessandra Villa <
> alessandra.villa.bio...@gmail.com>:
>
> > HI,
> >
> > On Tue, Dec 3, 2019 at 3:56 PM Александр Лашков 
> > wrote:
> >
> > > Dear gromacs team, you wrote in documentation "This information is
> needed
> > > for later free energy analysis if the states of interest are at
> different
> > > temperatures. If all states are at the same temperature, this
> information
> > > is not needed. ‘potential’ is useful in case one is using mdrun -rerun
> to
> > > generate the dhdl.xvg file.". But reduced potential used for MBAR
> > analysis
> > > include energy term and pV (for Gibs energy for NPT-ensemble) and
> > chemical
> > > potential (for grand canonical ensemble). All the same, is it necessary
> > or
> > > not necessary to save energy in dhdh files?
> > >
> >
> > You do not need the  mdp option "dhdl-print-energy"  if you are
> performing
> > free energy calculation at one temperature.
> >
> > Best regards
> > Alessandra
> >
> >
> >
> > > Sincerely,
> > > Alexander Lashkov
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
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> > > posting!
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Re: [gmx-users] Help installing do_x3dna

[Christian Blau]

Hi Salvador,


If you did not have any luck so far, trying to contact the author of the tool, 
Rajendra Kumar, directly might help:

https://scholar.google.com/citations?user=zYKuBCcJ&hl=en


Best,
Christian

On 2019-11-21 21:00, Salvador Herrera-Velarde wrote:

Dear All,

I am trying to install do_x3dna in a Linux (Ubuntu Mint) computer where I
have already installed gromacs-2019.2.

I followed the steps in:
https://do-x3dna.readthedocs.io/en/latest/install_do_x3dna.html
but without success.

I executed the following command:
cmake .. -DGMX_PATH=/usr/local/gromacs/
-DFFTW_LIB=/home/shv/Gromacs/gromacs-2019.2/Build/src/external/build-fftw/fftwBuild-prefix/lib/
make
without warnings... then I executed
sudo make install
I got the following error
make: *** No rule to make target 'install'.  Stop.

I had checked the do_x3dna forum but it seems outdated and there is no much
information there.

Any suggestion of how to install do_x3dna would be greatly appreciated

Thanks a lot
s h.v

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Re: [gmx-users] How to calculate the spatial distribution function for the last 50ns of the trajectory?

[Christian Blau]

Hi Peiyin,


There is a related redmine entry that suggests this might be fixed in newer versions of GROMACS 
https://redmine.gromacs.org/issues/2189


(from GROMACS2018 on). If you are using a newer GROMACS version, to rule out that this is an issue related to .tng, can 
you try using the older .xtc format instead?



Best,
Chrstian

On 2019-12-05 03:13, Peiyin Lee wrote:

Dear users,

I have a simulation that has a 400 ns trajectory and I would like to
calculate the spatial distribution function of the last 50ns. I followed
the instructions on gmx_spatial manual and everything was ok if I run the
first 50ns of the trajectory instead of the last 50 ns. However, once I
changed the command from gmx_mpi trjconv -s md.tpr -f md.xtc -b 0 -e 5
-o b.tng -boxcenter tric -ur compact -pbc none
to gmx_mpi trjconv -s md.tpr -f md.xtc -b 35 -e 40 -o b.tng
-boxcenter tric -ur compact -pbc none
and then ran gmx_mpi trjconv -s md.tpr -f b.tng  -o c.tng -fit rot+trans
I would get an error saying:

WARNING: Incomplete frame: nr 0 time 0


WARNING no output, last frame read at t=0

I have checked my trajectory with gmx_check and the trajectory is fine. I
wonder why those two commands only work with -b 0, but not -b anyothertime.
Does anyone have an idea? Thank you in advance!

Regards,
Peiyin

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