Re: [gmx-users] Dynamics only for cavity in molecule.

[Mark Abraham]

Hi,

I have no idea whether that will help. Even if it is better, I am
struggling to see that annealing and freeze groups is a useful model, even
with frozen solvent.

Mark

On Fri, 4 Aug 2017 21:40  wrote:

> Well, that means that I need to use the group scheme?
> Or I can just add solvent and run the same thing?
>
> > Hi,
> >
> > I imagine nobody has ever tried with Verlet plus freeze plus annealing,
> so
> > it could be broken somehow... But frozen atoms around a cavity and no
> > electric field from solvent sounds like a model highly unlikely to be
> > related to reality...
> >
> > Mark
> >
> > On Fri, 4 Aug 2017 18:55  wrote:
> >
> >> Hello!
> >>
> >> I want to run dynamics only for a relatively small cavity of my
> >> molecule,
> >> with all other atoms frozen. For this reason, I also don't use solvent,
> >> because it won't move anyway. I run the simulation on GPU (gromacs
> >> 5.1.2),
> >> i.e. I use the Verlet scheme, pbc = xyz. However, when I start running
> >> simulations, I get violent behavior: the molecule immediately falls
> >> apart!! I am sure that I just made a silly thing in the parameters, but
> >> what is it? Here I attach my dynamics .mdp parameters:
> >>
> >>
> >> define = -DPOSRES
> >> integrator = md
> >> dt = 0.001
> >> nsteps = 120
> >>
> >> nstxout = 1000
> >> nstvout = 1000
> >> nstxtcout = 1000
> >> nstlog = 100
> >> nstenergy = 1000
> >>
> >> continuation   = no
> >> constraints= none
> >>
> >> tcoupl = V-rescale
> >> tc_grps = System
> >> tau_t = 0.1
> >> ref_t = 0
> >>
> >> cutoff-scheme = Verlet
> >> ns_type   = grid
> >> nstlist   = 10
> >> rcoulomb  = 0.9
> >> rvdw  = 0.9
> >>
> >> coulombtype   = PME
> >> pme_order = 4
> >> fourierspacing = 0.16
> >>
> >> pbc  = xyz
> >> gen_vel  = no
> >>
> >> DispCorr = EnerPres
> >>
> >> ;
> >> ; Freezing atoms # this is all the atoms except for the cavity inside
> >> ;
> >> freezegrps = GroupDyna
> >> freezedim = Y Y Y
> >> ;
> >> ; Heating
> >> ;
> >> annealing = single
> >> annealing_npoints = 2
> >> annealing_time = 0 50
> >> annealing_temp = 0 298
> >>
> >>
> >> Thank you in advance,
> >> Dmitrii.
> >>
> >>
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
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> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
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Re: [gmx-users] Dynamics only for cavity in molecule.

[nikolaev]

Well, that means that I need to use the group scheme?
Or I can just add solvent and run the same thing?

> Hi,
>
> I imagine nobody has ever tried with Verlet plus freeze plus annealing, so
> it could be broken somehow... But frozen atoms around a cavity and no
> electric field from solvent sounds like a model highly unlikely to be
> related to reality...
>
> Mark
>
> On Fri, 4 Aug 2017 18:55  wrote:
>
>> Hello!
>>
>> I want to run dynamics only for a relatively small cavity of my
>> molecule,
>> with all other atoms frozen. For this reason, I also don't use solvent,
>> because it won't move anyway. I run the simulation on GPU (gromacs
>> 5.1.2),
>> i.e. I use the Verlet scheme, pbc = xyz. However, when I start running
>> simulations, I get violent behavior: the molecule immediately falls
>> apart!! I am sure that I just made a silly thing in the parameters, but
>> what is it? Here I attach my dynamics .mdp parameters:
>>
>>
>> define = -DPOSRES
>> integrator = md
>> dt = 0.001
>> nsteps = 120
>>
>> nstxout = 1000
>> nstvout = 1000
>> nstxtcout = 1000
>> nstlog = 100
>> nstenergy = 1000
>>
>> continuation   = no
>> constraints= none
>>
>> tcoupl = V-rescale
>> tc_grps = System
>> tau_t = 0.1
>> ref_t = 0
>>
>> cutoff-scheme = Verlet
>> ns_type   = grid
>> nstlist   = 10
>> rcoulomb  = 0.9
>> rvdw  = 0.9
>>
>> coulombtype   = PME
>> pme_order = 4
>> fourierspacing = 0.16
>>
>> pbc  = xyz
>> gen_vel  = no
>>
>> DispCorr = EnerPres
>>
>> ;
>> ; Freezing atoms # this is all the atoms except for the cavity inside
>> ;
>> freezegrps = GroupDyna
>> freezedim = Y Y Y
>> ;
>> ; Heating
>> ;
>> annealing = single
>> annealing_npoints = 2
>> annealing_time = 0 50
>> annealing_temp = 0 298
>>
>>
>> Thank you in advance,
>> Dmitrii.
>>
>>
>> --
>> 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
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>> send a mail to gmx-users-requ...@gromacs.org.
>>
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[gmx-users] error at nvt equilibrium

[Mohammad Zahidul Hossain Khan]

Dear Sir

I am getting the error when I try for *gmx mdrun -deffnm nvt. *
I have attached my nvt.mdp. Can anyone help me about it

Double sids (1547, 1548) for atom 4837
Double sids (1547, 1548) for atom 4838
Double sids (1547, 1548) for atom 4839
Double sids (1547, 1548) for atom 4840
Double sids (1547, 1548) for atom 4841
Double sids (1547, 1548) for atom 4842
Double sids (1547, 1548) for atom 4843
Double sids (1547, 1548) for atom 4844
Double sids (1547, 1548) for atom 4845
Double sids (1547, 1548) for atom 4846
Double sids (1547, 1548) for atom 4847
Double sids (1547, 1548) for atom 4848
Double sids (1547, 1548) for atom 4849

---
Program gmx mdrun, VERSION 5.1.2
Source code file:
/build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/topology/invblock.c, line:
98

Fatal error:
Double entries in block structure. Item 3963 is in blocks 1548 and 1547
 Cannot make an unambiguous inverse block



-- 


*Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
*Email: khan5...@vandals.uidaho.edu *
* Skype: parash.khan2*
*Cell: +12085967165*
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Re: [gmx-users] Dynamics only for cavity in molecule.

[Mark Abraham]

Hi,

I imagine nobody has ever tried with Verlet plus freeze plus annealing, so
it could be broken somehow... But frozen atoms around a cavity and no
electric field from solvent sounds like a model highly unlikely to be
related to reality...

Mark

On Fri, 4 Aug 2017 18:55  wrote:

> Hello!
>
> I want to run dynamics only for a relatively small cavity of my molecule,
> with all other atoms frozen. For this reason, I also don't use solvent,
> because it won't move anyway. I run the simulation on GPU (gromacs 5.1.2),
> i.e. I use the Verlet scheme, pbc = xyz. However, when I start running
> simulations, I get violent behavior: the molecule immediately falls
> apart!! I am sure that I just made a silly thing in the parameters, but
> what is it? Here I attach my dynamics .mdp parameters:
>
>
> define = -DPOSRES
> integrator = md
> dt = 0.001
> nsteps = 120
>
> nstxout = 1000
> nstvout = 1000
> nstxtcout = 1000
> nstlog = 100
> nstenergy = 1000
>
> continuation   = no
> constraints= none
>
> tcoupl = V-rescale
> tc_grps = System
> tau_t = 0.1
> ref_t = 0
>
> cutoff-scheme = Verlet
> ns_type   = grid
> nstlist   = 10
> rcoulomb  = 0.9
> rvdw  = 0.9
>
> coulombtype   = PME
> pme_order = 4
> fourierspacing = 0.16
>
> pbc  = xyz
> gen_vel  = no
>
> DispCorr = EnerPres
>
> ;
> ; Freezing atoms # this is all the atoms except for the cavity inside
> ;
> freezegrps = GroupDyna
> freezedim = Y Y Y
> ;
> ; Heating
> ;
> annealing = single
> annealing_npoints = 2
> annealing_time = 0 50
> annealing_temp = 0 298
>
>
> Thank you in advance,
> Dmitrii.
>
>
> --
> Gromacs Users mailing list
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> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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[gmx-users] Dynamics only for cavity in molecule.

[nikolaev]

Hello!

I want to run dynamics only for a relatively small cavity of my molecule,
with all other atoms frozen. For this reason, I also don't use solvent,
because it won't move anyway. I run the simulation on GPU (gromacs 5.1.2),
i.e. I use the Verlet scheme, pbc = xyz. However, when I start running
simulations, I get violent behavior: the molecule immediately falls
apart!! I am sure that I just made a silly thing in the parameters, but
what is it? Here I attach my dynamics .mdp parameters:


define = -DPOSRES
integrator = md
dt = 0.001
nsteps = 120

nstxout = 1000
nstvout = 1000
nstxtcout = 1000
nstlog = 100
nstenergy = 1000

continuation   = no
constraints= none

tcoupl = V-rescale
tc_grps = System
tau_t = 0.1
ref_t = 0

cutoff-scheme = Verlet
ns_type   = grid
nstlist   = 10
rcoulomb  = 0.9
rvdw  = 0.9

coulombtype   = PME
pme_order = 4
fourierspacing = 0.16

pbc  = xyz
gen_vel  = no

DispCorr = EnerPres

;
; Freezing atoms # this is all the atoms except for the cavity inside
;
freezegrps = GroupDyna
freezedim = Y Y Y
;
; Heating
;
annealing = single
annealing_npoints = 2
annealing_time = 0 50
annealing_temp = 0 298


Thank you in advance,
Dmitrii.


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[gmx-users] MnO2 periodic system

[gangotri dey]

Dear all,

I am trying to equilibrate a MnO2 surface (not cluster periodic). After the
NVT run, I see that the surface is deformed. I was wondering what else can
I add in my nvt.mdp to not encounter this problem?

I have mainly followed the examples in the forum for graphene/CNT growth.

title   = MnO2  in H2O NVT equilibration
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 5 ; 2 * 50 = 100 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 50; save coordinates every 0.10 ps
nstvout = 50; save velocities every 0.10 ps
nstenergy   = 50; save energies every 0.10 ps
nstlog  = 50; update log file every 0.10 ps
; Bond parameters
continuation= no; first dynamics run
constraint_algorithm= lincs ; holonomic constraints
constraints = none  ; 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 = SOL MnO ; three 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
periodic-molecules = yes
; 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= 18; generate a random seed



*Thank you*

*Gangotri Dey*
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Re: [gmx-users] question about gmx do_dssp

[Mark Abraham]

Hi,

Isn't that figure what is in the xpm file?

Mark

On Fri, Aug 4, 2017 at 4:20 PM YanhuaOuyang <15901283...@163.com> wrote:

> Hi,
>I have run a MD simulation and used gmx do_dssp to calculate the
> secondary structure content. The output files are md_dssp.xpm and
> scount.xvg. I want to know that each residue  belongs to what kind of
> secondary structure for each frame. But the scount.xvg output file only
> have the number of residues with each secondary structure and the total
> secondary structure count as a function of time. So,  can I get the
> information on "each residue belongs to which kind of secondary structure
> for each frame" to draw a figure of " amino acid vs secondary structure" ?
>
> Best regards,
> Ouyang
> --
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Re: [gmx-users] Problem with dihedral restraints

[Mark Abraham]

Hi,

You should expect changes, you're not freezing the angles in place. You're
making it less energetically favourable for them to change. But if the
environment is strong enough, they'll respond to that. Increase kfac by a
factor of a thousand and they'll probably not move noticeably. Whether that
is a good idea is something you might find out later :-)

Mark

On Fri, Aug 4, 2017 at 4:16 PM gangotri dey  wrote:

> Hello!
>
> I posted a question a few days back and I got a reply but it still does not
> work.
>
> I have a small drug molecule that I would like to compute. I want to
> restraint the Ramachandran dihedral angles. I have used the following lines
> in the .itp file for the molecule. It was suggested that I increase the
> force constant, which I did. However, I still see the change in the
> dihedral angles after the NVT, NPT and Production run. I am not sure how
> best it can be implemented.
>
>
>
> [ dihedral_restraints ]
> ; ai   ajakal  type  phi  dphi  kfac
> 698 702 692 691 1 -142.56 0 100
> 719 712 716 698 1 -84.24 0 100
>
> 702698716712 150.3766 0 100
> 695691692702 1  -166.8294 0 100
>
>
> My .mdp file is similar to the one used in the Bevan lab tutorial online.
>
>
>
>
> *Thank you*
>
> *Gangotri Dey*
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Re: [gmx-users] Problem with dihedral restraints

[gangotri dey]

Thank you for the kind reply. I will compute and update in the post.



*Thank you*

*Gangotri Dey*
Postdoctoral Associate
Rutgers University New Brunswick
Chemistry and Chemical Biology
174 Frelinghuysen Road, Piscataway, NJ 08854
Phone: +16092162254




On Fri, Aug 4, 2017 at 10:31 AM, Mark Abraham 
wrote:

> Hi,
>
> You should expect changes, you're not freezing the angles in place. You're
> making it less energetically favourable for them to change. But if the
> environment is strong enough, they'll respond to that. Increase kfac by a
> factor of a thousand and they'll probably not move noticeably. Whether that
> is a good idea is something you might find out later :-)
>
> Mark
>
> On Fri, Aug 4, 2017 at 4:16 PM gangotri dey  wrote:
>
> > Hello!
> >
> > I posted a question a few days back and I got a reply but it still does
> not
> > work.
> >
> > I have a small drug molecule that I would like to compute. I want to
> > restraint the Ramachandran dihedral angles. I have used the following
> lines
> > in the .itp file for the molecule. It was suggested that I increase the
> > force constant, which I did. However, I still see the change in the
> > dihedral angles after the NVT, NPT and Production run. I am not sure how
> > best it can be implemented.
> >
> >
> >
> > [ dihedral_restraints ]
> > ; ai   ajakal  type  phi  dphi  kfac
> > 698 702 692 691 1 -142.56 0 100
> > 719 712 716 698 1 -84.24 0 100
> >
> > 702698716712 150.3766 0 100
> > 695691692702 1  -166.8294 0 100
> >
> >
> > My .mdp file is similar to the one used in the Bevan lab tutorial online.
> >
> >
> >
> >
> > *Thank you*
> >
> > *Gangotri Dey*
> > --
> > Gromacs Users mailing list
> >
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> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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> >
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[gmx-users] question about gmx do_dssp

[YanhuaOuyang]

Hi,
   I have run a MD simulation and used gmx do_dssp to calculate the secondary 
structure content. The output files are md_dssp.xpm and scount.xvg. I want to 
know that each residue  belongs to what kind of secondary structure for each 
frame. But the scount.xvg output file only have the number of residues with 
each secondary structure and the total secondary structure count as a function 
of time. So,  can I get the information on "each residue belongs to which kind 
of secondary structure for each frame" to draw a figure of " amino acid vs 
secondary structure" ?

Best regards,
Ouyang
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[gmx-users] Problem with dihedral restraints

[gangotri dey]

Hello!

I posted a question a few days back and I got a reply but it still does not
work.

I have a small drug molecule that I would like to compute. I want to
restraint the Ramachandran dihedral angles. I have used the following lines
in the .itp file for the molecule. It was suggested that I increase the
force constant, which I did. However, I still see the change in the
dihedral angles after the NVT, NPT and Production run. I am not sure how
best it can be implemented.



[ dihedral_restraints ]
; ai   ajakal  type  phi  dphi  kfac
698 702 692 691 1 -142.56 0 100
719 712 716 698 1 -84.24 0 100

702698716712 150.3766 0 100
695691692702 1  -166.8294 0 100


My .mdp file is similar to the one used in the Bevan lab tutorial online.




*Thank you*

*Gangotri Dey*
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Re: [gmx-users] Error in itp file

[Souvik Dey]

You can use this link for ACPYPE:

http://webapps.ccpn.ac.uk/acpype/

First, you have to mail the author and then he would give you a user ID and
password.

On Fri, Aug 4, 2017 at 1:48 AM, Justin Lemkul  wrote:

>
>
> On 8/3/17 8:53 AM, Souvik Dey wrote:
>
>> ​Yes, I saw the GROMACS website. But my itp file has [atomtypes] first
>> followed by [moleculetypes]. So, I am still not getting what is the
>> error.​
>>
>>
> All [atomtypes] (and more generally, any force field parameters) must
> appear before *any* [moleculetype] directives, not just the one to which
> the parameters apply.  So a topology that introduces parameters must be
> #included before any invocation of a [moleculetype].
>
> -Justin
>
>
> On Thu, Aug 3, 2017 at 2:52 PM, Souvik Dey  wrote:
>>
>> Yes, using ACPYPE is pretty simple. They have a web server, where you can
>>> upload your PDB or MOL2 file, provide the charge and multiplicity and it
>>> gives you the output file.
>>>
>>> On Wed, Aug 2, 2017 at 7:03 PM, Justin Lemkul  wrote:
>>>
>>>

 On 8/2/17 12:35 PM, Souvik Dey wrote:

 Hi,
>
> I just generated an itp file from ACPYPE. However, if I try to add ions
> it
> shows the following error:
>
> Fatal error:
> Syntax error - File FAD.itp, line 3
> Last line read:
> '[ atomtypes ]'
> Invalid order for directive atomtypes
>
>
> Can somebody say how do I fix this?
>
>
> This exact situation is described here:

 http://www.gromacs.org/Documentation/Errors#Invalid_order_fo
 r_directive_xxx

 -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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>>>
>>>
>>> --
>>> Souvik Dey
>>> Integrated Science Education & Research Centre
>>> Visva Bharati University
>>> Santiniketan-731235
>>> West Bengal
>>> 8981736643
>>>
>>>
>>
>>
>>
> --
> ==
>
> 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
>
> ==
> --
> Gromacs Users mailing list
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>



-- 
Souvik Dey
Integrated Science Education & Research Centre
Visva Bharati University
Santiniketan-731235
West Bengal
8981736643
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[gmx-users] Could not find clayff forcefield

[G R]

Dear users,

I try to implement Clayff forcefield for Kaolinite. I created my force
field (I'm not sure about it), but gromacs couldn't find my force field in
the directory. Here is my forcefield.

ffnonbonded
[ atomtypes ]
; name   mass  chargeptype  sigma  eps
 HW   1  1.00800 0.4100A0.0e-01  0.0e-01
;clayFF_waterhydrogen
 HO   1  1.00800 0.4250A0.0e-01  0.0e-01
;clayFF_hydroxylhydrogen
 OW   8 15.99800-0.8200A3.16557e-01  6.50209e-01
;ClayFF_wateroxygen
 OH   8 15.99800-0.9500A3.16557e-01  6.50209e-01
;ClayFF_hydroxyloxygen
 OB   8 15.99800-1.0500A3.16557e-01  6.50209e-01
;ClayFF_bridgingoxygen
 OBOS 8 15.99800-1.1808A3.16557e-01  6.50209e-01
;ClayFF_bridgingoxygenoctasub
 OBTS 8 15.99800-1.1688A3.16557e-01  6.50209e-01
;ClayFF_bridgingoxygentetrsub
 OHS  8 15.99800-1.0808A3.16557e-01  6.50209e-01
;ClayFF_hydroxyloxygensub
 SI  14 28.08600 2.1000A3.30208e-01  8.0e-06
;ClayFF_tetrahedralsilicon
 AO  13 26.98200 1.5750A4.27128e-01  6.0e-06
;ClayFF_octahedalaluminium
 AT  13 26.98200 1.5750A3.30206e-01  8.0e-06
;ClayFF_tetrasubaluminium

ffbonded
[ bondtypes ]
; ij  func   b0  kb
 OW HW   10.1000 554134.9
 OH HO   10.1000 554134.9
 OHSHO   10.1000 554134.9

[ angletypes ]
;  ijk  func   th0   cth
 HW   OWHW1109.47191.564
 AL   OHHO1109.47125.52

atomtype.n2t
HHW0.4100 1.008  1O  0.100 ;water hydrogen
OOW   -0.820015.998  2H  0.100H  0.100 ;water oxygen
OH2  OH   -0.950015.998  1H  0.100 ;hydroxyl oxygen
O2   obts  -1.1688  15.998  0;bridging oxygen with
tetrahedral substitution
O1   obss  -1.2996  15.998  0 ;bridging oxygen with
double substitution
OH1  ohs   -1.0808   15.998  1  H  0.100   ;hydroxyl hydrogen with
substitution
Si   st2.100028.086  0 ;tetrahedral silicon
Al   ao1.575026.982  0 ;octahedral aluminium
Mg  mgo1.360024.305  0 ; octahedral magnisium
Na   Na1.22.999  0 ;sodium ion

forcefield.doc
clayff.ff force field

forcefield.itp
#define _ff_clayff


[ defaults ]
 ; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
 1   3   yes 0.5 0.5

#include "ffnonbonded.itp"
#include "ffbonded.itp"

pdb

Al0.6494.3333.377
Al3.248.8053.377
Al3.2032.8513.362
Al0.6397.3243.362
Si4.9623.0160.65
Si2.3987.4880.65
Si2.4421.470.653
Si-0.1225.9420.653
O1-0.3343.0982.268
O12.2587.572.268
O10.0415.8392.271
O12.6051.3672.271
O30.0144.4720
O3-1.8854.2597.154
O35.1694.4720
O33.274.2597.154
O32.57800
O30.678-0.2147.154
O32.6058.9450
O30.7068.7317.154
O31.0342.0560.177
O33.6266.5290.177
O31.0526.8480.023
O33.6162.3760.023
OH1-0.3228.6062.304
OH12.2424.1332.304
OH23.831.364.329
OH21.2665.8324.329
OH2-0.9624.1364.35
OH21.6298.6084.35
OH2-0.9617.5354.36
OH21.6023.0634.36
O22.63310.3122.271
OH23.85810.3054.329
OH24.8348.6062.304
OH24.1947.5354.36
O34.8213.0982.268
OH34.1934.1364.35
O36.192.0560.177
O3-1.5296.5290.177


It's to long, Sorry about it, but I really need to find out where is my
problem. I put n2t file in directory not in my forcefield subdirectory. Do
I need to create any other file for clayff forcefield?

Thank you in advece,
Golnaz
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[gmx-users] The small organic molecule occurred deformation during simulation

[yujie liu]

Hello, users
 
I’m a novice to study the gromacs program. Now I met some problems which the 
small molecule occurred deformation when energy minimization was performed. For 
example, the anthracene molecule became bent in the plane of C-rings, the same 
as phenol. I want to know whether  the situation is normal? In addition, I 
employed gromos54a7.ff

Yours sincerely

Yujie liu

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Re: [gmx-users] Does gmx distance correct for broken molecules from pbc?

[Mark Abraham]

Hi,

gmx help distance shows that there are two PBC-related options. Perhaps
your answer lies there.

Mark

On Fri, Aug 4, 2017 at 9:47 AM Ramon Crehuet 
wrote:

> Dear all,
>
> I have a system composed of a trimeric protein and a double stranded DNA.
> I would like to calculate the distance between the center of mass (com) of
> the protein and the com of the DNA (I am working with the NVT equilibration
> trajectory as an example). I tried:
>
>
> gmx distance -f nvt.trr -s nvt.tpr -select 'com of group Protein plus cog
> of group DNA' -xvg none -oall -rmpbc
>
> This gave distances that seem too long. Then I created a trajectory
> removing the PBC:
>
> gmx trjconv -f em.gro -s em.tpr -o whole.pdb -pbc nojump
> gmx trjconv -f nvt.trr -o whole.xtc -s whole.pdb -pbc nojump
>
> And calculated the distances again:
>
> gmx distance -f whole.xtc -s whole.pdb -select 'com of group Protein plus
> cog of group DNA' -xvg none -oall -rmpbc
>
> This gives reasonable results, different from the previous call to gmx
> distance. In an attempt to avoid calculating the whole.xtc trajectory I
> gave a pdb file that doesn't have broken molecules:
>
> gmx distance -f nvt.trr -s whole.pdb -select 'com of group Protein plus
> cog of group DNA' -xvg none -oall -rmpbc
>
> But this still gives the wrong result. I thought the flag -rmpbc would
> make molecules whole, but apparently it doesn't in my case. Is there a way
> to calculate the distance directly from the original trajectory?
>
>
> Thanks in advance,
>
> Ramon
>
>
>
> --
>
>
> Ramon Crehuet
>
> Cientific Titular (Assistant Professor)
>
> Institute of Advanced Chemistry of Catalonia IQAC - CSIC
>
> scholar.google.es/citations?user=PIHmEiwJ
> orcid.org/-0002-6687-382X
> publons.com/a/1018637/
> twitter.com/rcrehuet
> ramoncrehuet.wordpress.com
>
> Tel. +34 934006116 <+34%20934%2000%2061%2016>
> Jordi Girona 18-26
> 08034 Barcelona (Spain)
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[gmx-users] Does gmx distance correct for broken molecules from pbc?

[Ramon Crehuet]

Dear all, 

I have a system composed of a trimeric protein and a double stranded DNA. I 
would like to calculate the distance between the center of mass (com) of the 
protein and the com of the DNA (I am working with the NVT equilibration 
trajectory as an example). I tried: 


gmx distance -f nvt.trr -s nvt.tpr -select 'com of group Protein plus cog of 
group DNA' -xvg none -oall -rmpbc 

This gave distances that seem too long. Then I created a trajectory removing 
the PBC: 

gmx trjconv -f em.gro -s em.tpr -o whole.pdb -pbc nojump 
gmx trjconv -f nvt.trr -o whole.xtc -s whole.pdb -pbc nojump 

And calculated the distances again: 

gmx distance -f whole.xtc -s whole.pdb -select 'com of group Protein plus cog 
of group DNA' -xvg none -oall -rmpbc 

This gives reasonable results, different from the previous call to gmx 
distance. In an attempt to avoid calculating the whole.xtc trajectory I gave a 
pdb file that doesn't have broken molecules: 

gmx distance -f nvt.trr -s whole.pdb -select 'com of group Protein plus cog of 
group DNA' -xvg none -oall -rmpbc 

But this still gives the wrong result. I thought the flag -rmpbc would make 
molecules whole, but apparently it doesn't in my case. Is there a way to 
calculate the distance directly from the original trajectory? 


Thanks in advance, 

Ramon 



-- 


Ramon Crehuet 

Cientific Titular (Assistant Professor) 

Institute of Advanced Chemistry of Catalonia IQAC - CSIC 

scholar.google.es/citations?user=PIHmEiwJ 
orcid.org/-0002-6687-382X 
publons.com/a/1018637/ 
twitter.com/rcrehuet 
ramoncrehuet.wordpress.com 

Tel. +34 934006116 
Jordi Girona 18-26 
08034 Barcelona (Spain)
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