date:20191021

Re: [gmx-users] Frozen group moves!

2019-10-21 Thread Alex

Hi,
Thanks for the response.

On Tue, Oct 22, 2019 at 02:04 David van der Spoel 
wrote:

> Den 2019-10-21 kl. 21:24, skrev Alex:
> > Dear all,
> > I freeze a group in my system in all directions as normal:
> > freezegrps   = GR
> > freezedim= Y Y Y
> > So, I was expecting that the coordinates and velocities do not get
> updated
> > during the simulation, however, here is just part of in.gro and out.gro
> in
> > which the coordinates and velocity components have changed.
> >  #Y  #Z   #Vx #Vy   #Vz
> >#Y  #Z   #Vx #Vy   #Vz
> >0.271   0.049  0.  0.  0.|  0.271
> >   0.050  0.  0. -0.0637
> >0.249   0.020  0.  0.  0.|  0.249
> >   0.020  0.  0.  0.1823
> >0.251   0.490  0.  0.  0.|  0.251
> >   0.490  0.  0. -0.6805
> >0.228   0.524  0.  0.  0.|  0.228
> >   0.524  0.  0. -0.1568
> >0.251   0.055  0.  0.  0.|  0.251
> >   0.055  0.  0. -0.4114
> >0.369  17.054  0.  0.  0.|  0.369
> > 17.055  0.  0. -0.5276
> >0.390   0.272  0.  0.  0.|  0.390
> >   0.273  0.  0. -0.2386
> >0.184   0.444  0.  0.  0.|  0.184
> >   0.444  0.  0. -0.1694
> >0.365   0.444  0.  0.  0.|  0.365
> >   0.444  0.  0.  0.1299
> >0.361   0.553  0.  0.  0.|  0.361
> >   0.554  0.  0. -0.5277
> >
> > Anybody knows what might be the reason and how one can avoid that to
> happen?
> >
> > Regards,
> > Alex
> >
> Do you have pressure coupling turned on?
> Alternatively, are the frozen coordinates part of a compound that is
> constrained?
> Both of these could cause this.

No, the simulation is in NVT ensemble by which I am trying to heat up the
system from room temperature to 443 K. However before heating, the system
had been equlibrated for 1 ns NVT and 2 ns NPT (1ns berendsen and 1 ns
parrinello rahman) by semi-isotropic. In equilibration everything was fine.

No it isn’t, the frozen group is not constrained.

Regards,
Alrx

>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Head of Department, Cell & Molecular Biology, Uppsala University.
> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> http://www.icm.uu.se
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Frozen group moves!

2019-10-21 Thread David van der Spoel


Den 2019-10-21 kl. 21:24, skrev Alex:

Dear all,
I freeze a group in my system in all directions as normal:
freezegrps   = GR
freezedim= Y Y Y
So, I was expecting that the coordinates and velocities do not get updated
during the simulation, however, here is just part of in.gro and out.gro in
which the coordinates and velocity components have changed.
 #Y  #Z   #Vx #Vy   #Vz
   #Y  #Z   #Vx #Vy   #Vz
   0.271   0.049  0.  0.  0.|  0.271
  0.050  0.  0. -0.0637
   0.249   0.020  0.  0.  0.|  0.249
  0.020  0.  0.  0.1823
   0.251   0.490  0.  0.  0.|  0.251
  0.490  0.  0. -0.6805
   0.228   0.524  0.  0.  0.|  0.228
  0.524  0.  0. -0.1568
   0.251   0.055  0.  0.  0.|  0.251
  0.055  0.  0. -0.4114
   0.369  17.054  0.  0.  0.|  0.369
17.055  0.  0. -0.5276
   0.390   0.272  0.  0.  0.|  0.390
  0.273  0.  0. -0.2386
   0.184   0.444  0.  0.  0.|  0.184
  0.444  0.  0. -0.1694
   0.365   0.444  0.  0.  0.|  0.365
  0.444  0.  0.  0.1299
   0.361   0.553  0.  0.  0.|  0.361
  0.554  0.  0. -0.5277

Anybody knows what might be the reason and how one can avoid that to happen?

Regards,
Alex


Do you have pressure coupling turned on?
Alternatively, are the frozen coordinates part of a compound that is 
constrained?

Both of these could cause this.

--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation

2019-10-21 Thread Amit Jaiswal

Dear Jorden, Thanks for your reply. As you have suggested, i found there is a mismatch of the atom number in the zn.itp file and the .gro file. I have included few residues of .gro file for your convenience.   What i understand is that I have to rename the zn.itp file with residue no. 4265 and not 2220. Please correct me if I am wrong. And also you suggested me to "minimize the system very carefully". What do you mean by this? Should i use lesser minimisation steps ? Thanks for your time and efforts. With kind regards,Amit 391THR HG22 4260 4.897 5.356 3.136391THR HG23 4261 4.889 5.247 2.993391THR C 4262 4.600 5.071 3.244391THR OT1 4263 4.599 5.012 3.355391THR OT2 4264 4.496 5.082 3.173392ZN ZN 4265 7.278 6.612 5.838393NAD PA 4266 6.217 7.359 2.802393NAD O1A 4267 6.090 7.410 2.863393NAD O2A 4268 6.337 7.451 2.808393NAD O5B 4269 6.185 7.331 2.647393NAD C5B 4270 6.082 7.233 2.620   19.10.2019, 21:53, "Jorden Cabal" :Dear Amit,Your files look correct to me. If "2220" atom in your coordinate file isthe "Zn" atom, it should not be displaced because, from your mdp file andtopology setting you have restrained all the heavy atoms of Protein, Nadand Zn. I don't understand why it is happening. Even the restraining forceyou are taking is good enough.I suggest you to check if the atom number 2220 in the co-ordinate file(.gro file) is Zn atom or not? If it is not then you have wrongly selectedatom number for restraining. Also, if you are following the standardtutorial for energy minimization which do not restrain any atom, I suggestyou to check the position of Zn atom in structure you get after energyminimization. If the location of Zn ion is changed during the EM, then youwill need to minimize the system very carefully.Hope this will fix your issue.Thank you--Gromacs Users mailing list* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists* For (un)subscribe requests visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.   -- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Frozen group moves!

2019-10-21 Thread Alex

Dear all,
I freeze a group in my system in all directions as normal:
freezegrps   = GR
freezedim= Y Y Y
So, I was expecting that the coordinates and velocities do not get updated
during the simulation, however, here is just part of in.gro and out.gro in
which the coordinates and velocity components have changed.
#Y  #Z   #Vx #Vy   #Vz
  #Y  #Z   #Vx #Vy   #Vz
  0.271   0.049  0.  0.  0.|  0.271
 0.050  0.  0. -0.0637
  0.249   0.020  0.  0.  0.|  0.249
 0.020  0.  0.  0.1823
  0.251   0.490  0.  0.  0.|  0.251
 0.490  0.  0. -0.6805
  0.228   0.524  0.  0.  0.|  0.228
 0.524  0.  0. -0.1568
  0.251   0.055  0.  0.  0.|  0.251
 0.055  0.  0. -0.4114
  0.369  17.054  0.  0.  0.|  0.369
17.055  0.  0. -0.5276
  0.390   0.272  0.  0.  0.|  0.390
 0.273  0.  0. -0.2386
  0.184   0.444  0.  0.  0.|  0.184
 0.444  0.  0. -0.1694
  0.365   0.444  0.  0.  0.|  0.365
 0.444  0.  0.  0.1299
  0.361   0.553  0.  0.  0.|  0.361
 0.554  0.  0. -0.5277

Anybody knows what might be the reason and how one can avoid that to happen?

Regards,
Alex
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Problem on pbc atom

2019-10-21 Thread Justin Lemkul





On 10/19/19 12:48 PM, Mahsa Rezaei wrote:

Dear gromacs users,
I am using following pull code in md simulation
for pulling a ligand across the plasma membrane model.
My size box is 8.52807   8.52807  14.0.
And the pull distance is less than one-half the length of the box vector
along.pull distance is 6 nm.


when I execute this command,I got warning:

gmx grompp -f md_pull.mdp -c complex.gro -p topol.top -r complex.gro -n
index.ndx -o pull.tpr


WARNING 1 [file md_pull.mdp]:
   Pull group 1 has atoms at a distance larger than 0.9 times half the box
   size from the PBC atom (27119). If atoms are or will more beyond half the
   box size from the PBC atom, the COM will be ill defined.

Pull group  natoms  pbc atom  distance at start  reference at t=0
1 54231 27120
2 4 2  -3.769 nm -3.769 nm
Estimate for the relative computational load of the PME mesh part: 0.10
This run will generate roughly 1238 Mb of data

Fatal error:
Too many warnings (1).
If you are sure all warnings are harmless, use the -maxwarn option.

What should I do?
I would be very appreciated for your such kind helps.


The reference for determining periodic distances is simply the numerical 
middle of the atom selection, which may not have any resemblance to the 
geometric center. If your group(s) is(are) non-spherical in nature, you 
need to select an appropriate atom for grompp and mdrun to compute the 
periodic distances.


-Justin


My mdp file  :

integrator  = md
dt  = 0.002
nsteps  = 29 ; 580 ps
; Output parameters
nstlog  = 1000
nstxout = 500   ; every 1 ps
nstvout = 500
nstfout = 500
nstxtcout   = 500; every 1 ps
nstcalcenergy   = 500
nstenergy   = 500

cutoff-scheme   = Verlet
nstlist = 20
rlist   = 1.2
coulombtype = pme
rcoulomb= 1.2
vdwtype = Cut-off
vdw-modifier= Force-switch
rvdw_switch = 1.0
rvdw= 1.2
;
tcoupl  = Nose-Hoover
tc_grps = PROT  MEMB_LIG  SOL_ION
tau_t   = 1.01.01.0
ref_t   = 303.15 303.15 303.15
;
pcoupl  = Parrinello-Rahman
pcoupltype  = semiisotropic
tau_p   = 5.0
compressibility = 4.5e-5  4.5e-5
ref_p   = 1.0 1.0
;
constraints = h-bonds
constraint_algorithm= LINCS
continuation= yes
;
nstcomm = 100
comm_mode   = linear
comm_grps   = PROT MEMB_LIG SOL_ION
;
refcoord_scaling= com

; Pull code
pull   = yes
pull_ncoords   = 1 ; only one reaction coordinate
pull_ngroups   = 2
pull_group1_name   = BILAYER
pull_group2_name   = LIG
pull_coord1_type   = umbrella  ; harmonic potential
pull_coord1_geometry   = direction
pull_coord1_vec= 0.0 0.0 1.0
pull_coord1_groups = 1 2
pull_coord1_start  = yes   ; define initial COM distance > 0
pull_coord1_rate   = 0.01  ; 0.01 nm per ps =10nm per ns
pull_coord1_k  = 2000  ; kJ mol^-1 nm^-2
pull_nstxout   = 500; every 1 ps
pull_nstfout   = 500; every 1 ps





[image: Mailtrack]

Sender
notified by
Mailtrack

10/19/19,
08:14:02 PM


--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Solvation of protein on membrane surface

2019-10-21 Thread Justin Lemkul





On 10/20/19 5:57 AM, Olga Press wrote:

Prof. Lemkul,
Thank you very much for your reply. I would be very grateful if you can
help me with some questions regarding voids compression.
Should I run the NPT equilibration on the whole system( including
protein+membrame+solvent +*ions*) meaning, should I continue my protocol
(adding ions-->NVT equilibration with position restraints on the
protein---> and than NPT equilibration with position restraints---> NPT
equilibration without restraints) or should I run first NPT
equilibration without position restraints (and for how long?) and than
continue the protocol?


A normal protocol with restraints on your protein should work fine. 
Those voids will be gone within tens of picoseconds.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Intermolecular Nonbonded Interactions

2019-10-21 Thread Justin Lemkul




On 10/21/19 8:04 AM, Batuhan Kav wrote:

Dear Al

lI have a question regarding the non-bonded LJ interactions between two 
molecules. In particular about how Gromacs generates the non bonded LJ 
interactions between the water and protein molecules.

In my system I am using a custom forcefield for the water molecules and 
Charmm36 for the protein. My intention is to change the epsilon/sigma LJ 
parameters between the water atoms and the protein atoms.

For the sake of a simple test I use spc water model (spc.itp) to solvate the 
protein. As far as I can see in the ffnonbonded.itp there is the correct atom 
type for the spc water (in the [ atomtypes ] directive) defined however it 
lacks the protein-water atom pairs in the [ pairtypes ] section. This makes me 
think that when I run grompp it will generate the non bonded LJ interaction 
values between the protein and water atoms following the combination rule in 
the forcefield.itp file provided gen-pairs is set to “yes”. When I set 
gen-pairs to “no” I expected that grompp will complain that the LJ pairs for 
the water atom and protein atoms are missing. However grompp runs without any 
warnings/errors and the simulation can be started.

Therefore my question is: how does Gromacs generate nonbonded interaction 
between the molecules if no specific atom-atom pairs are provided in the 
[pairtypes] and gen-pairs is “no”  (these atom-atom pairs are not defined 
anywhere in any part of the forcefield at all)?


Pairs refer specifically to intramolecular 1-4 interactions, so they are 
irrelevant for what you're trying to. Some force fields have special 
rules about whether or not special parameters are generated in these 
cases or omitted entirely if not listed in [pairtypes]. What you want to 
do is implement an NBFIX via the [nonbond_params] directive, which we 
list as a separate nbfix.itp file in the C36 port for GROMACS.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Question about default auto setting of mdrun -pin

2019-10-21 Thread aeszter

On Fri, Oct 18, 2019 at 04:54:49PM +0200, Szilárd Páll wrote:
> 
> The source of total number of hardware threads should not be OpenMP but a
> system call or hwloc -- which should (and was IIRC a while ago at least)
> checked agianst the  gmx_omp_nthreads_get() value.

Yes, that's correct. The number of *hw threads* is determined from
hwloc (if it's compiled in), and the number of mdrun threads is from
OpenMP.

However, the default assumption of OpenMP is that you have the whole
node, and mdrun then concludes that pinning is OK.

A.

-- 
Ansgar Esztermann
Sysadmin Dep. Theoretical and Computational Biophysics
http://www.mpibpc.mpg.de/grubmueller/esztermann
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Intermolecular Nonbonded Interactions

2019-10-21 Thread Batuhan Kav

Dear Al

lI have a question regarding the non-bonded LJ interactions between two 
molecules. In particular about how Gromacs generates the non bonded LJ 
interactions between the water and protein molecules.

In my system I am using a custom forcefield for the water molecules and 
Charmm36 for the protein. My intention is to change the epsilon/sigma LJ 
parameters between the water atoms and the protein atoms.

For the sake of a simple test I use spc water model (spc.itp) to solvate the 
protein. As far as I can see in the ffnonbonded.itp there is the correct atom 
type for the spc water (in the [ atomtypes ] directive) defined however it 
lacks the protein-water atom pairs in the [ pairtypes ] section. This makes me 
think that when I run grompp it will generate the non bonded LJ interaction 
values between the protein and water atoms following the combination rule in 
the forcefield.itp file provided gen-pairs is set to “yes”. When I set 
gen-pairs to “no” I expected that grompp will complain that the LJ pairs for 
the water atom and protein atoms are missing. However grompp runs without any 
warnings/errors and the simulation can be started.

Therefore my question is: how does Gromacs generate nonbonded interaction 
between the molecules if no specific atom-atom pairs are provided in the 
[pairtypes] and gen-pairs is “no”  (these atom-atom pairs are not defined 
anywhere in any part of the forcefield at all)?

I’m sorry if this is a trivial question but I am rather confused about this.

Best,
Batuhan
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Frozen group moves!

Re: [gmx-users] Frozen group moves!

Re: [gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation

[gmx-users] Frozen group moves!

Re: [gmx-users] Problem on pbc atom

Re: [gmx-users] Solvation of protein on membrane surface

Re: [gmx-users] Intermolecular Nonbonded Interactions

Re: [gmx-users] Question about default auto setting of mdrun -pin

[gmx-users] Intermolecular Nonbonded Interactions

9 matches

Site Navigation

Mail list logo

Footer information