[gmx-users] Distance between atom A and the nearest image of atom B

[Michael Cristòfol Clough]

Hello everyone,

I'm writing a little program and I want to calculate the distance between
atom A and the nearest image of atom B. I imagine a function is already
implemented but I can't find it, could anybody tell me what it's called?

Thank you in advance,

Michael
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Re: [gmx-users] Fwd: Help with Gromacs 5.1 mdp options for CHARMM27 force field

[Rakesh Ramachandran]

Hi Justin,

Thanks for the reply. Sorry if I am asking too many questions. I wanted
to clarify some more doubts just to make sure I am performing the
simulation the right way.

1) What is the ideal Tcoupl option for CHARMM36 Nose-hoover or V-rescale.
Moreover I get the following note and warning when I use Nose-Hoover
thermostat.

NOTE 1 [file npt.mdp]:
  leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1

WARNING 1 [file npt.mdp]:
  For proper integration of the Nose-Hoover thermostat, tau-t (1) should be
  at least 20 times larger than nsttcouple*dt (0.08)

So is V-rescale more optimal for Verlet cutoff and GPU based Gromacs.

2) Moreover I see in some publications that 0.9 nm to 1.0 nm for minimum
protein-edge distance is being used for Gromacs. Even in your tutorial you
mention using 1.0 nm. Taking into account minimum image convention should
it not be greater than 1.2 nm or is it highly dependent on the protein you
are simulating or rcouloumb cutoff or is dependent on Debye length.

I would be grateful if you could clear my doubts on this aspect or point me
to the relevant literature. I am planning to use 1.25 nm for a salt conc of
300 mM MgCl2 with epsilon_r = 1 or should I use higher cutoff such as 1.4
nm. Moreover is the dielectric constant of the medium 82 for TIP3P water
model at 300K (ref http://www1.lsbu.ac.uk/water/water_models.html),

3) In spite of running the NPT equilibration for 5 ns I am getting these
values and the RMSD values are also too high when the pressure parameter is
measured. In your tutorial you had suggested to run longer NPT
equilibration if the density value does not converge to around 1000 kg/m^3
and pressure value around 1 bar. I found the same issue when I ran with
CHARMM27 force field and V-rescale thermostat. But on plotting I find the
results are similar to your plots in the tutorial but for 5 ns in both the
cases (CHARMM 27 and 36).

for 1.25 nm protein-edge distance

Pressure1.52207   0.52146.1081.62992  (bar)
Density 1056.64  0.029 2.7515 -0.0336808
 (kg/m^3)

for 1.4 nm protein-edge distance

Pressure   0.321022   0.94137.028 2.4858  (bar)
Density 1054.45  0.0532.67943   0.264365
 (kg/m^3)

Regards
Rakesh


On 4 December 2015 at 18:04, Justin Lemkul  wrote:

>
>
> On 12/3/15 6:55 AM, Rakesh Ramachandran wrote:
>
>> Hi Justin,
>>
>> Thanks for the reply. I have doubts regarding pdb2gmx options are
>> the chargegrp and cmap options required while generating topology file
>> when
>> using CHARMM36 force field and do these options have any effect.
>>
>>
> CHARMM does not use charge groups; every atom is its own group.  Moreover,
> charge groups are ignored when using the Verlet cutoff scheme (which you
> need to be, to use the settings I provided).  The [ cmap ] directives are
> required if you want to actually use CMAP for the backbone, which is an
> integral part of the force field.
>
> Moreover I saw in your recent paper "Phosphorylation of PPARγ Affects
>> the Collective Motions of the PPARγ-RXRα-DNA Complex", you had used H++
>> web
>> server to assign protonation state. The server generates only PDB file and
>> AMBER topology file so how can I use this in Gromacs. I would be grateful
>>
>
> Well, we used an AMBER force field for those simulations, so using an
> AMBER-prepared coordinate file is seamless.  The important part is the set
> of pKa values and subsequent protonation states.  You can set these using
> pdb2gmx interactively (read the help information).
>
> if you could share the code or script for PCA based energy landscape
>> generation shown in your paper as I am also interested in the collective
>> dynamics.
>>
>>
> If you wish to discuss my work specifically, please contact me offline
> rather than posting to the mailing list and boring everyone else :)  The
> PCA is a straightforward application of gmx covar and gmx anaeig.  There's
> nothing special there.
>
> Also I want to retain crystallographic water and ions, but I see the
>> box
>> size increases and also see that the naming is different HOH for
>> crystallographic water and SOL for TIP3P.  Will this have any effect or is
>> it always better to remove any crystallographic water or ions before
>> simulating.
>>
>>
> Depends on whether or not those waters are structurally relevant.  Usually
> there is no harm in keeping them, sometimes removing something important in
> a binding/active site is inappropriate.
>
> -Justin
>
>
>
>> On 1 December 2015 at 18:14, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 11/30/15 3:17 PM, Rakesh Ramachandran wrote:
>>>
>>> Hi Justin,

   Thanks for the reply. I have few more doubts. I had mentioned
 CHARMM27
 just for consistency with Gromacs naming. In the website it mentions
 that
 those settings are for CHARMM36 and I read at lot of places that this

Re: [gmx-users] extracting coordinates from traj.xtc

[Justin Lemkul]

On 12/6/15 2:49 AM, mah maz wrote:

Thank you. I tested gmxdump and also trjconv -dump and compared traj.trr
and traj.xtc. You are right both have the same data. I just need the
coordinates to be readable a printable in a file now. Although I can write
a program to extract the coordinates from gmxdump the way I need, it seems
a bit time consuming. And I couldn't find a way yet! Is there a command
like g_traj -f traj.trr -ox to print coordinates from traj.xtc?


Frankly, from the information you're providing (which is vague at best) there is 
nothing I can tell you that will be any use.  The coordinates in .trr and .xtc 
cannot be different (outside of the fact that they are different precision).  It 
is not logical that one file differs from the other unless one of them is 
somehow corrupt.  If the trajectories load fine (e.g. in VMD), gmxcheck reports 
no problems, and coordinate files dumped out of them agree, there is no 
explanation for why you think you have junk coordinates coming out of g_traj. 
You've reported a single number that seems to be wrong but no other context, so 
it's impossible to diagnose this further.


-Justin


Thanks!

On Thu, Dec 3, 2015 at 8:27 PM, mah maz  wrote:


Thanks Justin! I checked the run and it seemed ok. The fact is, the data I
get by g_traj -f traj.trr -ox is reasonable (although I didnt set nstxout
it was set every 100 step by default), while the same command with g_traj
-f traj.xtc -ox gives wrong coordinates. Since I need coordinates for every
step I need to extract them from traj.xtc. Can you suggest any ways?

Thank you!

On Tue, Dec 1, 2015 at 4:51 PM, mah maz  wrote:


Thank you Justin. I expected that only water molecules are written in
.xtc but all the others are there! g_traj -f traj.xtc -ox gives numbers
like 1.64e-318 for all frames! How can I get real coordinates from .xtc?
Thanks!

On Tue, Dec 1, 2015 at 10:34 AM, mah maz  wrote:


Dear all,
I have some problems extracting data from traj.xtc. The command " g_traj
-s -ox" doesn't give reasonable coordinates. I tried "trjconv" but
again couldn't get any results.  Note that I have nstxtcout = 1 and xtc_
grps = water in my .mdp file.
Any help is appreciated.
Thank you!








--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] water sorient

[xy21hb]

Dear all, I would like to calculate the water orientation near ubiqutin by 
gmx_sorient, gmx sorient -f md.trr -s md.tpr -o -no -ro -co -rc

first, the sord.xvg shows the angle (i.e. theta 1) between the vector1 (nearest 
heavy protein atom to water oxygen) and
vector 2 (water oxygen to the mid of of water hydrogen 1 and 2) is mostly 90 
degrees, isn't that weird?
I would expect water dipole more or less pointing to or away from the vector 1, 
depending on the charge of the heavy atom.

2nd, sori.xvg second column should be the distribution of cos (theta1), but it 
shows some value greater than 1.

Any ideas?

Thanks,

Yao
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Re: [gmx-users] Fwd: Help with Gromacs 5.1 mdp options for CHARMM27 force field

[Justin Lemkul]

On 12/6/15 8:57 AM, Rakesh Ramachandran wrote:

Hi Justin,

 Thanks for the reply. Sorry if I am asking too many questions. I wanted
to clarify some more doubts just to make sure I am performing the
simulation the right way.

1) What is the ideal Tcoupl option for CHARMM36 Nose-hoover or V-rescale.
Moreover I get the following note and warning when I use Nose-Hoover
thermostat.



Use either; there is no force field dependence here.


NOTE 1 [file npt.mdp]:
   leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1



Notes are for information only; they do not indicate a problem.


WARNING 1 [file npt.mdp]:
   For proper integration of the Nose-Hoover thermostat, tau-t (1) should be
   at least 20 times larger than nsttcouple*dt (0.08)



Check your settings here.  Warnings are important.


So is V-rescale more optimal for Verlet cutoff and GPU based Gromacs.

2) Moreover I see in some publications that 0.9 nm to 1.0 nm for minimum
protein-edge distance is being used for Gromacs. Even in your tutorial you
mention using 1.0 nm. Taking into account minimum image convention should
it not be greater than 1.2 nm or is it highly dependent on the protein you
are simulating or rcouloumb cutoff or is dependent on Debye length.



As long as the minimum image convention is not violated, there is no problem. 
Using a minimum solute-box distance equal to the longest cutoff is safe, but 
overkill.  1.0 nm is typically sufficient because then there are at least 2.0 nm 
between image atoms of, e.g. a protein, which is a couple of solvent shells and 
therefore enough.



I would be grateful if you could clear my doubts on this aspect or point me
to the relevant literature. I am planning to use 1.25 nm for a salt conc of
300 mM MgCl2 with epsilon_r = 1 or should I use higher cutoff such as 1.4
nm. Moreover is the dielectric constant of the medium 82 for TIP3P water
model at 300K (ref http://www1.lsbu.ac.uk/water/water_models.html),



Do not touch epsilon_r.  Leave it at 1.  It is not the dielectric constant; it 
is the reference for dielectric screening.  If you change this value, you change 
in vacuo screening in a manner inconsistent with real physics and the force 
field parametrization.



3) In spite of running the NPT equilibration for 5 ns I am getting these
values and the RMSD values are also too high when the pressure parameter is
measured. In your tutorial you had suggested to run longer NPT
equilibration if the density value does not converge to around 1000 kg/m^3
and pressure value around 1 bar. I found the same issue when I ran with
CHARMM27 force field and V-rescale thermostat. But on plotting I find the
results are similar to your plots in the tutorial but for 5 ns in both the
cases (CHARMM 27 and 36).

for 1.25 nm protein-edge distance

Pressure1.52207   0.52146.1081.62992  (bar)
Density 1056.64  0.029 2.7515 -0.0336808
  (kg/m^3)

for 1.4 nm protein-edge distance

Pressure   0.321022   0.94137.028 2.4858  (bar)
Density 1054.45  0.0532.67943   0.264365
  (kg/m^3)



Welcome to life when trying to simulate pressure.

http://www.gromacs.org/Documentation/Terminology/Pressure

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] extracting coordinates from traj.xtc

[Justin Lemkul]

On 12/6/15 2:56 AM, mah maz wrote:

And also, if I want velocities for every step what can I do?


nstvout = 1

-Justin


Thanks!

On Sun, Dec 6, 2015 at 11:19 AM, mah maz  wrote:


Thank you. I tested gmxdump and also trjconv -dump and compared traj.trr
and traj.xtc. You are right both have the same data. I just need the
coordinates to be readable a printable in a file now. Although I can write
a program to extract the coordinates from gmxdump the way I need, it
seems a bit time consuming. And I couldn't find a way yet! Is there a
command like g_traj -f traj.trr -ox to print coordinates from traj.xtc?
Thanks!

On Thu, Dec 3, 2015 at 8:27 PM, mah maz  wrote:


Thanks Justin! I checked the run and it seemed ok. The fact is, the data
I get by g_traj -f traj.trr -ox is reasonable (although I didnt set nstxout
it was set every 100 step by default), while the same command with g_traj
-f traj.xtc -ox gives wrong coordinates. Since I need coordinates for every
step I need to extract them from traj.xtc. Can you suggest any ways?

Thank you!

On Tue, Dec 1, 2015 at 4:51 PM, mah maz  wrote:


Thank you Justin. I expected that only water molecules are written in
.xtc but all the others are there! g_traj -f traj.xtc -ox gives numbers
like 1.64e-318 for all frames! How can I get real coordinates from .xtc?
Thanks!

On Tue, Dec 1, 2015 at 10:34 AM, mah maz  wrote:


Dear all,
I have some problems extracting data from traj.xtc. The command " g_
traj -s -ox" doesn't give reasonable coordinates. I tried "trjconv"
but again couldn't get any results.  Note that I have nstxtcout = 1
and xtc_grps = water in my .mdp file.
Any help is appreciated.
Thank you!










--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] atom numbering

[Marta Wisniewska]

Dear Gromacs users,

My problem focus on number order. I am preparing my system to md. In my pdb
file I made a some modifications (delete chains or ligand compounds).
During preparation of topology and gro file, the residue number ordering is
changed. Is there any possibility to preserve number ordering from pdb file
during pdb2gmx transfer?

Thank you in advance,
Marta
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Re: [gmx-users] atom numbering

[Peter Stern]

Justin already answered your question five days ago:
Use the -norenum option for pdb2gmx

Peter

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Marta 
Wisniewska
Sent: Sunday, December 06, 2015 2:03 PM
To: gmx-us...@gromacs.org
Subject: [gmx-users] atom numbering

Dear Gromacs users,

My problem focus on number order. I am preparing my system to md. In my pdb 
file I made a some modifications (delete chains or ligand compounds).
During preparation of topology and gro file, the residue number ordering is 
changed. Is there any possibility to preserve number ordering from pdb file 
during pdb2gmx transfer?

Thank you in advance,
Marta
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Re: [gmx-users] center

[Tsjerk Wassenaar]

Hi Malihe,

Check the suggested trjconv workflow at
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Cheers,

Tsjerk

On Sun, Dec 6, 2015 at 12:39 PM, Malihe Hasanzadeh 
wrote:

> Hi
> I have run a ligand-protein MD simulation for 50 ns by gromacs 5.0.5. At
> the end of simulations, molecule is out of the box.I have used from two
> below command for center but neither of them isn't work and molecule still
> is out of box.
>
> trjconv -f md300.trr -o md300t.xtc -fit rot+trans -s md300.tpr
> trjconv -f md300.trr -o md300t.xtc -pbc mol -center -s md300.tpr
>
> So how to center the molecule before going for analysis?
> Thanks
> --
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>



-- 
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[gmx-users] center

[Malihe Hasanzadeh]

Hi
I have run a ligand-protein MD simulation for 50 ns by gromacs 5.0.5. At
the end of simulations, molecule is out of the box.I have used from two
below command for center but neither of them isn't work and molecule still
is out of box.

trjconv -f md300.trr -o md300t.xtc -fit rot+trans -s md300.tpr
trjconv -f md300.trr -o md300t.xtc -pbc mol -center -s md300.tpr

So how to center the molecule before going for analysis?
Thanks
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Re: [gmx-users] Getting too much time to finish nvt equilibrium, why?

[Tsjerk Wassenaar]

Hi Surya,

We can't say from this information. The log files should give more insight.
Was the computer being used for something else at the same time?

Cheers,

Tsjerk
On Dec 7, 2015 05:52, "Seera Suryanarayana"  wrote:

> Dear Gromacs Users,
>
> After energy minimization I have done nvt equilibrium for 1ns. It has taken
> 15 to 20 minutes when I done it previously. Same equilibrium I did day
> before yesterday and it has take almost one day. I have used the same work
> station in both equilibrium processes. I have used the following mdp file.
> System consists 129 residue length protein and more the three 3,00,000
> water molecules. Kindly check the mdp file and let me how to resolve this
> long lasting processes.
>
>
> define  = -DPOSRES  ; position restrain the protein
> ; Run parameters
> integrator  = md; leap-frog integrator
> nsteps  = 50; 2 * 50 = 1000 ps
> dt  = 0.002 ; 2 fs
> ; Output control
> nstxout = 5000  ; save coordinates every 10.0 ps
> nstvout = 5000  ; save velocities every 10.0 ps
> nstenergy   = 5000  ; save energies every 10.0 ps
> nstlog  = 5000  ; update log file every 10.0 ps
> ; Bond parameters
> continuation= no; first dynamics run
> constraint_algorithm= lincs ; holonomic constraints
> constraints = all-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= 1.0   ; short-range electrostatic cutoff
> (in nm)
> rvdw= 1.0   ; short-range van der Waals cutoff
> (in nm)
> ; 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= EnerPres  ; 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
>
>
> Thanks in advance
>
> Surya
> Graduate student
> India.
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[gmx-users] Getting too much time to finish nvt equilibrium, why?

[Seera Suryanarayana]

Dear Gromacs Users,

After energy minimization I have done nvt equilibrium for 1ns. It has taken
15 to 20 minutes when I done it previously. Same equilibrium I did day
before yesterday and it has take almost one day. I have used the same work
station in both equilibrium processes. I have used the following mdp file.
System consists 129 residue length protein and more the three 3,00,000
water molecules. Kindly check the mdp file and let me how to resolve this
long lasting processes.


define  = -DPOSRES  ; position restrain the protein
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 50; 2 * 50 = 1000 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 5000  ; save coordinates every 10.0 ps
nstvout = 5000  ; save velocities every 10.0 ps
nstenergy   = 5000  ; save energies every 10.0 ps
nstlog  = 5000  ; update log file every 10.0 ps
; Bond parameters
continuation= no; first dynamics run
constraint_algorithm= lincs ; holonomic constraints
constraints = all-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= 1.0   ; short-range electrostatic cutoff
(in nm)
rvdw= 1.0   ; short-range van der Waals cutoff
(in nm)
; 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= EnerPres  ; 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


Thanks in advance

Surya
Graduate student
India.
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