Re: [gmx-users] [gmx-developers] How to put two molecules inside the simulation box with a control on their DISTANCE and ANGLE

[Dallas Warren]

GROMACS Users emailing list more appropriate for this question.

You can used editconf to translate, rotate coordinates around.  So
move the 2nd one around, then copy / paste the coordinates into the
1st coordinate file, making sure adjust the atom number count and
maintain the correct header/footer format.  Another option is loading
into vmd and manually moving the molecules around, then saving the
coordinates.
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 13 February 2018 at 10:41, Armin Solemanifar
 wrote:
> Dear Gromacs users,
>
> I'm trying to put two peptides inside the simulation box and have the
> ability to rotate them to face each other in a particular way before
> starting the simulation. I only know how to put them randomly in the
> simulation box.
>
> My second question is how to put them in a certain distance from each other
> in the beginning as well.
>
> Cheers,
> Armin
>
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Re: [gmx-users] KALP 15 in model membrane

[Armin Solemanifar]

Hi,

Putting capping on the peptide/protein end affect the its polarity and you
should check how it could affect your protein structure or whether you want
it to be charged or not at the tails.

Cheers,
Armin

On Mon, Feb 12, 2018 at 9:39 PM, Negar Parvizi 
wrote:

> Dear all Gromacs usersI have started the tutorial on membrane protein,
> provided by Justin ( KALP 15 in model membrane).Now I have two questions:1)
> Why Justin adds the ACE and NH2 groups to the two ends of the peptide model?
> The -ter option in pdb2 gmx command can add interactively the NH2 or NH3+
> , and COOH or COO- to the N and C terminies.What is the preference of ACE
> over COO- or COOH?
> 2) The next question is: How should I decide to add which of the mentioned
> groups to the N or C terminies, when simulating the transmembrane protein??
> Thanks in advance for your timeNegar
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Re: [gmx-users] tune_pme error with GROMACS 2018

[Daniel Kozuch]

Carsten,

I was hoping yo use tune_pme to optimize a REMD job across multiple nodes,
so I think I need it compiled with MPI (please let me know if that logic is
incorrect).
I am indeed running on GPU nodes (I tested mdrun on the nodes and and there
was no issue).

Best,
Dan

On Mon, Feb 12, 2018 at 8:32 AM, Kutzner, Carsten  wrote:

> Hi Dan,
>
> > On 11. Feb 2018, at 20:13, Daniel Kozuch  wrote:
> >
> > Hello,
> >
> > I was recently trying to use the tune_pme tool with GROMACS 2018 with the
> > following command:
> >
> > gmx tune_pme -np 84 -s my_tpr.tpr -mdrun 'gmx mdrun’
> Maybe you need to compile gmx without MPI (so that gmx tune_pme
> is a serial executable), and a separate mdrun which naturally
> needs to be MPI-enabled (the latter you pass via -mdrun argument).
>
> >
> > but I'm getting the following error:
> >
> > "Fatal error:
> > Cannot execute mdrun. Please check benchtest.log for problems!"
> >
> > Unfortunately benchtest.log is an empty file. I saw that there were some
> > similar problems with GROMACS 5. Is this still an issue?
> What output is there on the command line?
>
> Are you running on GPU nodes? Are all shared libraries needed by
> mdrun actually found?
>
> Best,
>   Carsten
>
>
> >
> > Thanks,
> > Dan
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>
> --
> Dr. Carsten Kutzner
> Max Planck Institute for Biophysical Chemistry
> Theoretical and Computational Biophysics
> Am Fassberg 11, 37077 Goettingen, Germany
> Tel. +49-551-2012313, Fax: +49-551-2012302
> http://www.mpibpc.mpg.de/grubmueller/kutzner
> http://www.mpibpc.mpg.de/grubmueller/sppexa
>
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[gmx-users] charmm36 force field

[farial tavakoli]

Dear GMX users
I used charmm36 force field to run MD simulation on my receptor and ligand 
which has 2 phosphotyrosine groups. All of steps that I did are following as:

1) gmx pdb2gmx -f .pdb -o .gro -water tip4p -ignh -his2) gmx editconf -f .gro 
-o newbox.gro -c -d 1.0 -bt dodecahedron3)gmx solvate -cp newbox.gro -cs 
tip4p.gro -p .top -o .gro 4) gmx grompp -f ions.mdp -c .gro -p .top -o 
ions.tpr5) gmx genion -s ions.tpr -o .gro -p .top -pname NA -np 11 -nname CL6) 
gmx frompp -f minim.mdp -c .gro -p .top -o em.tpr7) gmx mdrun -v -deffnm em
ions.mdp and minim.mdp files:; minim.mdp - used as input into grompp to 
generate em.tpr
integrator    = steep        ; Algorithm (steep = steepest descent minimization)
emtol        = 1000.0      ; Stop minimization when the maximum force < 1000.0 
kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps        = 5          ; Maximum number of (minimization) steps to 
perform

; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions
nstlist        = 1        ; Frequency to update the neighbor list and 
long range forces
cutoff-scheme   = Verlet
ns_type        = grid        ; Method to determine neighbor list (simple, 
grid)
coulombtype    = PME        ; Treatment of long range electrostatic 
interactions
rcoulomb    = 1.2        ; Short-range electrostatic cut-off
rvdw        = 1.2        ; Short-range Van der Waals cut-off
vdwtype = cutoff
vdw-modifier = force-switch
rvdw-switch = 1.0
pbc        = xyz         ; Periodic Boundary Conditions (yes/no)
DispCorr = no

then I checked em.gro using vmd, the ligand was in the active site and there 
was no problem.
8) gmx grompp -f nvt.mdp -c em.gro -p .top -o nvt.tpr9) gmx mdrun -deffnm nvt
nvt.mdp file:
title        = CHARMM36 EGFR NVT equilibration 
define        =  -DUSE_OLD_C3
; Run parameters
integrator    = md        ; leap-frog integrator
nsteps        = 20        ; 2 * 5 = 400 ps
dt        = 0.002        ; 2 fs
; Output control
nstxout        = 500        ; save coordinates every 1.0 ps
nstvout        = 500        ; save velocities every 1.0 ps
nstenergy    = 500        ; save energies every 1.0 ps
nstlog        = 500        ; update log file every 1.0 ps
; Bond parameters
continuation    = no        ; first dynamics run
constraint_algorithm    = lincs    ; holonomic constraints 
constraints    = h-bonds    ; all bonds (even heavy atom-H bonds) 
constrained
lincs_iter    = 1        ; accuracy of LINCS
lincs_order    = 4        ; also related to accuracy
; Neighborsearching
cutoff-scheme   = Verlet
ns_type        = grid        ; search neighboring grid cells
nstlist        = 10        ; 20 fs, largely irrelevant with Verlet
rcoulomb    = 1.2        ; short-range electrostatic cutoff (in nm)
rvdw        = 1.2        ; short-range van der Waals cutoff (in nm)
vdwtype = cutoff
vdw-modifier = force-switch
rlist = 1.2
rvdw-switch = 1.0
; Electrostatics
coulombtype    = PME    ; Particle Mesh Ewald for long-range electrostatics
pme_order    = 4        ; cubic interpolation
fourierspacing    = 0.16    ; grid spacing for FFT
; Temperature coupling is on
tcoupl        = V-rescale    ; modified Berendsen thermostat
tc-grps        = Protein Non-Protein    ; two coupling groups - more accurate
tau_t        = 0.1      0.1   ; time constant, in ps
ref_t        = 300       300   ; reference temperature, one for each 
group, in K
; Pressure coupling is off
pcoupl        = no         ; no pressure coupling in NVT
; Periodic boundary conditions
pbc        = xyz        ; 3-D PBC
; Dispersion correction
DispCorr    = no        ; account for cut-off vdW scheme
; Velocity generation
gen_vel        = yes        ; assign velocities from Maxwell distribution
gen_temp    = 300        ; temperature for Maxwell distribution
gen_seed    = -1        ; generate a random seed
but when I checked nvt.gro by VMD ,  viewed  the receptor and ligand went out 
of the box, almost completely and ligand was separated from the protein, 
completely. Is there anyone who can help me and advice me why it was happened?
best Farial
 



 
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[gmx-users] Parallelization in large system

[Rachel Baarda]

Dear Gromacs users,

I am trying to simulate a large system (roughly 3M atoms including solvent)
on Gromacs version 4.5.5. I am having difficulty having mdrun execute
parallel calculations. I have run several variations (described below) of
attempting steepest descent minimization and the simulation finishes
successfully only if I set the number of threads to just 1.

variation 1: mdrun -v -deffnm steep_to_1000
Result:
Making 1D domain decomposition grid 8 x 1 x 1, home cell index 0 0 0
Program mdrun, VERSION 4.5.5
Source code file: /share/apps/pkg/gromacs-4.5.5/src/mdlib/domdec_top.c,
line: 356
Fatal error:
8346 of the 4590648 bonded interactions could not be calculated because
some atoms involved moved further apart than the multi-body cut-off
distance (1 nm) or the two-body cut-off distance (1 nm), see option -rdd,
for pairs and tabulated bonds also see option -ddcheck

variation 2: mdrun -v -deffnm steep_to_1000 -noddcheck
Result: identical to variation 1 (6528 of the 4422192 bonded interactions
...)

variation 3: mdrun -v -deffnm steep_to_1000 -nt 1
Result:
Successfully finishes run without incident (but very slowly)

I also tested a simulation of a smaller system (~15k atoms), which ran
without incident on a 1D domain decomposition grid 8 x 1 x 1.

What parameters do you recommend I change to allow for multithreading?

Thank you in advance,

Rachel Baarda
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[gmx-users] Solvation energy estimation gmx sasa

[Krzysztof Makuch]

Hi,
I'd like to ask about solvation energy given in gmx sasa (gromacs 2016)
with option:
-odg
What algorithm is used here, or rather - what values are given for area of
particular atom types? I guess there is publication behind this, but the
only mentioned in gmx sasa focus on solvation area. Is it the paper written
by Eisenberg & McLchlan in 1985?
I know this is only rough estimation, but still I'd love if it could be
mentioned in program description.
Best,
Krzysiek Makuch

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[gmx-users] how can i restrain Zn ion during simulations

[vijayakumar gosu]

Dear gromacs users,


I am currently running simulations for protein-RNA complex. However i have
to include one Zn ion which is coordinated by 4 cysteine residues. when i
performed energy minimization itself zinc displaces. How can i restrain to
Zn, or to freeze Zn during simulations.

Thanks in advance


Best,

Vijayakumar Gosu
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Re: [gmx-users] REMD DLB bug

[Szilárd Páll]

Hi,

The fix will be released in an upcoming 2016.5 patch release. (which
you can see in the redmine issue page "Target version" field BTW).

Cheers,
--
Szilárd


On Mon, Feb 12, 2018 at 2:49 PM, Akshay  wrote:
> Hello All,
>
> I was running REMD simulations on Gromacs 2016.1 when my simulation crashed
> with the error
>
> Assertion failed:
> Condition: comm->cycl_n[ddCyclStep] > 0
> When we turned on DLB, we should have measured cycles
>
> I saw that there was a bug #2298 reported about this recently at
> https://redmine.gromacs.org/issues/2298. I wanted to know if this fix has
> been implemented in the latest 2018 or 2016.4 versions?
>
> Thanks,
> Akshay
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[gmx-users] REMD DLB bug

[Akshay]

Hello All,

I was running REMD simulations on Gromacs 2016.1 when my simulation crashed
with the error

Assertion failed:
Condition: comm->cycl_n[ddCyclStep] > 0
When we turned on DLB, we should have measured cycles

I saw that there was a bug #2298 reported about this recently at
https://redmine.gromacs.org/issues/2298. I wanted to know if this fix has
been implemented in the latest 2018 or 2016.4 versions?

Thanks,
Akshay
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[gmx-users] PBC

[Ahmed Mashaly]

Hi
If I want to use gmx trjconv to recenter the protein in xtc file, the reference 
(-s) .tpr should be the one I used in simulation (md.tpr) or I can use the 
first one (em.tpr) without a difference?

This is because the protein has jumped after em step, and if I have to use 
md.tpr as reference for md.xtc, I will have to recenter it after every step of 
em, nvt, npt
Kind Regards,Ahmed 

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Re: [gmx-users] tune_pme error with GROMACS 2018

[Kutzner, Carsten]

Hi Dan,

> On 11. Feb 2018, at 20:13, Daniel Kozuch  wrote:
> 
> Hello,
> 
> I was recently trying to use the tune_pme tool with GROMACS 2018 with the
> following command:
> 
> gmx tune_pme -np 84 -s my_tpr.tpr -mdrun 'gmx mdrun’
Maybe you need to compile gmx without MPI (so that gmx tune_pme
is a serial executable), and a separate mdrun which naturally
needs to be MPI-enabled (the latter you pass via -mdrun argument).

> 
> but I'm getting the following error:
> 
> "Fatal error:
> Cannot execute mdrun. Please check benchtest.log for problems!"
> 
> Unfortunately benchtest.log is an empty file. I saw that there were some
> similar problems with GROMACS 5. Is this still an issue?
What output is there on the command line?

Are you running on GPU nodes? Are all shared libraries needed by
mdrun actually found?

Best,
  Carsten


> 
> Thanks,
> Dan
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Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/grubmueller/kutzner
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Re: [gmx-users] Fwd: MMPBSA

[Wes Barnett]

On Fri, Feb 9, 2018 at 8:14 AM, RAHUL SURESH 
wrote:

> Dear all
>
> I have carried out a protein ligand simulation for 50ns and performed a
> PBSA calculation for 10-20ns trajectory. I get a positive binding energy.
> How can I tackle it..?
>
> Thank you
>
>
I think you haven't received in responses because it's unclear what you're
asking or what your problem is. You ran some kind of simulation and did a
PBSA calculation (not familiar with that) and got a positive binding
energy. You'll have to add more details on what you are attempting to
achieve, how you are trying to do so (perhaps including input scripts), and
what the exact problem is.

Wes


-- 
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Department of Chemical Engineering
Kumar Research Group 
Columbia University
w.barn...@columbia.edu
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Re: [gmx-users] Tests with Threadripper and dual gpu setup

[Harry Mark Greenblatt]

BS”D



Did you build with or without hwloc?

I did use hwloc.




—
Gromacs 2018 rc1 (using gcc 4.8.5)
—

Using AVX_256


You should be using AVX2_128 or AVX2_256 or Zen! The former will be fastest
in CPU-only runs, the latter can often be (a bit) faster in GPU accelerated
runs.


Once I saw that AVX2_128 was faster, I did not think there would be an 
advantage to AVX2_256 on GPU runs.

So is there any suggestion to overcome the problem of gcc 5.5 not recognising 
what CPU hardware I have (not that 5.5 gave much of an advantage in Gromacs 
2016).


Now force Dynamic Load Balancing

gmx mdrun -v -deffnm test.npt -s test.npt.tpr -pme gpu -pin on -ntmpi 4
-npme 1 -gputasks 0011 -nb gpu -dlb yes


I would recommend *against* doing that unless you have concrete cases where
this is better than "-dlb auto" -- and if you have such cases, please share
them as it is not expected behavior. (Note: DLB has acquired the capability
to observe when turning it on it leads to performance drop and it switches
off automatically in such cases!)


I did see that it in some cases it was turning off DLB for a while, or for the 
rest of the run.

In my case however, I did get better results by forcing it to be on.

I can send the .tpr file to you, off-list, if you want…



Thanks

Harry





Harry M. Greenblatt
Associate Staff Scientist
Dept of Structural Biology   
harry.greenbl...@weizmann.ac.il<../../owa/redir.aspx?C=QQgUExlE8Ueu2zs5OGxuL5gubHf97c8IyXxHOfOIqyzCgIQtXppXx1YBYaN5yrHbaDn2xAb8moU.=mailto%3aharry.greenblatt%40weizmann.ac.il>
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[gmx-users] Prolactin receptor in a mixed DPPC-DMPC bilayer

[Negar Parvizi]

Dear all Gromacs users, I want to simulate prolactin receptor in a mixed 
DPPC-DMPC bilayer. At first, I will insert the trans membrane part of the 
protein (prolactin receptor) in the bilayer and do the necessary modifications 
to the FF, according to the Justin,s membrane protein tutorial.
It should be mentioned that, the part of the prolactin receptor which connects 
to the prolactin, is out of membrane and has separate pdb code in OPM 
(orientations of Membrane Proteins) and protein data bank.Now the question:** 
How can I connect the out of membrane part of the prolactin receptor to its 
trans membrane part ( which has been inserted in the membrane).My goal is to 
simulate both transmembrane and out of membrane parts of the receptor 
simultaneously.
Thanks for your time and kind considerationNegar

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[gmx-users] KALP 15 in model membrane

[Negar Parvizi]

Dear all Gromacs usersI have started the tutorial on membrane protein, provided 
by Justin ( KALP 15 in model membrane).Now I have two questions:1) Why Justin 
adds the ACE and NH2 groups to the two ends of the peptide model?
The -ter option in pdb2 gmx command can add interactively the NH2 or NH3+ , and 
COOH or COO- to the N and C terminies.What is the preference of ACE over COO- 
or COOH?
2) The next question is: How should I decide to add which of the mentioned 
groups to the N or C terminies, when simulating the transmembrane protein??
Thanks in advance for your timeNegar
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Re: [gmx-users] pressure coupling error in umbrella sampling

[kordzadeh]

Hi Dr.Abraham

Thank you very much for your answer

yas I ve extacted configuration with 0.2 nm distance and when I want to 
run NPT for first configuration,I gave that error.

I didnt undersatnd this mdp file for this step, I got this file from 
umbrella sampling tutorial and I adjusted for my system but I didnt 
understand

we are doing a pullind simulation with zero velocity, I think the aim is to 
costriant structure by artifial spring but we dont  move it, am I right?

Thank you very mmuch for your anwer, your help and your time

Regards

Azadeh

 

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