Re: [gmx-users] Bug?! Lost particles while sorting

[Mohsen Ramezanpour]

Hi Mark,

Thanks for replying on this email.
I forgot to reply again and mention that it was not a bug.
I could fix it simply by following some instructions in:

https://docs.computecanada.ca/wiki/GROMACS

It is working perfectly fine now (GPU with version 2016.3)

Here are two things I changed in my script when submitted the jobs on the
cluster:
1) replacing "srun" with "mpiexec"
2) including the following line and removing the -ntomp  1 in mdrun command

export OMP_NUM_THREADS="${SLURM_CPUS_PER_TASK:-1}"

Cheers,
Mohsen


On Fri, Oct 13, 2017 at 4:02 AM, Mark Abraham 
wrote:

> Hi,
>
> Unfortunately that will just get lost in my inbox, and anyway I will have
> to go and make the redmine issue. We need that (rather than email) because
> multiple people might find the issue and need to be able to search for the
> answer. Also, somebody else fixing the issue won't be able to contact you
> easily if we need to follow up to get further information, or check that
> the issue is resolved.
>
> To file a request, please follow the link on https://redmine.gromacs.org/
> after
> you register an account. All quite easy, I hope! Do let us know if some
> aspect is hard.
>
> Mark
>
> On Thu, Aug 31, 2017 at 3:04 PM Mohsen Ramezanpour <
> ramezanpour.moh...@gmail.com> wrote:
>
> > Hi Mark,
> >
> > Thanks for your reply.
> > I tried but I was not sure how to do so.
> > May I send the corresponding files to your personal email, instead?
> >
> > Cheers,
> > Mohsen
> >
> >
> > On Wed, Aug 30, 2017 at 6:25 PM, Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > That particular output indicates that the code is not working as
> > intended.
> > > Please open an issue on the GROMACS redmine and attach the tpr, the log
> > > file from your run, and and instructions on how to reproduce.
> > >
> > > Thanks,
> > >
> > > Mark
> > >
> > > On Wed, 30 Aug 2017 19:34 Mohsen Ramezanpour <
> > ramezanpour.moh...@gmail.com
> > > >
> > > wrote:
> > >
> > > > Dear Gromacs users,
> > > >
> > > > I am running simulations using Gromacs version 2016.3 while using
> GPU.
> > > >
> > > > I get an error in my simulations as follows:
> > > >
> > > > Program: gmx mdrun, version 2016.3
> > > > Source file: src/gromacs/mdlib/nbnxn_grid.cpp (line 404)
> > > > MPI rank:15 (out of 16)
> > > >
> > > > Software inconsistency error:
> > > > Lost particles while sorting
> > > >
> > > > For more information and tips for troubleshooting, please check the
> > > GROMACS
> > > > website at http://www.gromacs.org/Documentation/Errors
> > > >
> > > >
> > > > Googling the error I found that there were relevant bugs before
> > > (discussed
> > > > by Dr. Berk Hess):
> > > >
> > > > https://redmine.gromacs.org/issues/1379
> > > >
> > > > https://redmine.gromacs.org/issues/1153
> > > >
> > > > However, they should have been fixed in the newer versions as
> mentioned
> > > in
> > > > the above links.
> > > >
> > > > Can someone please let me know what the problem could be in this
> case?
> > > >
> > > > Many thanks in advance,
> > > >
> > > > Cheers,
> > > > Mohsen
> > > > --
> > > > *Rewards work better than punishment ...*
> > > > --
> > > > 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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> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
> > > --
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> > >
> >
> >
> >
> > --
> > *Rewards work better than punishment ...*
> > --
> > Gromacs Users mailing list
> >
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*Rewards work better than punishment ...*
-- 
Gromacs Users mailing list

* Please 

Re: [gmx-users] Order Parameter for HII phase

[Mohsen Ramezanpour]

Hi Justin, Tom, Antonio,

I read the articles recommended in the previous emails.
To get the order parameter, for any system and by any technique (e.g.
g_angle), we need to calculate the C-D vector angle with respect to the
"local normal vector" at the place of that lipid.

For the bilayer, it is the Z direction which is the normal vector to the
bilayer surface. Easy.

For the HII, however, this "local normal vector" is challenging.
The cylinders in HII (which is long enough) are not perfect cylinders and
are bent (in a shape like a Tilda "~" ). Even when the cylinders are not
bent (i.e.they are like "__", still a "local normal vector" need to be
calculated in this calculation.


Here are four solutions I am thinking about:

1) Using the "radial" option in g_order, but I am not sure if this will
give what I want.

2) Slicing the HII cylinders in Z direction (i.e. the cylinder axis),
calculating a center of mass for those lipids in each slice, and then using
the g_angle and its "-g2 sphnorm". In this way, the COM of that slice will
be taken as the center of the sphere (an approximation).

3) Using g_angle but using "-g1 plane": in this case, the coordinates of
three atoms in that lipid at each frame will be used to make the local
normal vector.

4) Maybe a combination of g_sgangle and g_angle/g_order. The
g_sgangle seems to give the local normal vector for each time frame. This
can be subsequently used in g_order or g_angle for angle calculation.

One of the main problems in methods 3 and 4 is that: the way the three
atoms on the lipid are selected, the normal vector will be different,
especially if the lipid is tilted.

Is there any other way which I could calculate the C-D angle and order
parameter in HII phase?

Please let me know your opinion. Any help is appreciated in advance.

Cheers,
Mohsen

On Thu, Feb 23, 2017 at 4:55 PM, Mohsen Ramezanpour <
ramezanpour.moh...@gmail.com> wrote:

> Thanks Antonio.
> I will give them a try :-)
>
> Cheers
> Mohsen
>
> On Thu, Feb 23, 2017 at 4:15 PM, Antonio Baptista 
> wrote:
>
>> Hi Mohsen,
>>
>> I suggest you have a look at the QRB 1977 review by Seelig, that Tom
>> already mentioned. Like for the planar case, they discuss how spectra of
>> cylindrical lipid phases are related to the order parameter tensor (but I
>> never looked into the details for that case). Anyway, I don't know if you
>> want to compare your simulations with experimental data or are just looking
>> for a convenient structural parameter. But, whatever the case is, reading
>> the literature and thinking about the geometry of your system (Duliez's
>> papers are a good train for that) should give you some hints for a relevant
>> parameter for your system.
>>
>> Once you have selected a parameter, you can compute it from stratch using
>> other GROMACS tools besides g_order. In particular, you can use g_gangle to
>> get several sorts of angles and then process them yourself. As an example,
>> you can use this approach to compute SCD using the equation already
>> mentioned by Tom, and then check if it agrees with the SCD given by g_order
>> (I once did that, just to be sure).
>>
>> Good luck! :)
>>
>> Best,
>> Antonio
>>
>>
>>
>> On Thu, 23 Feb 2017, Justin Lemkul wrote:
>>
>>
>>>
>>> On 2/23/17 1:25 PM, Mohsen Ramezanpour wrote:
>>>
 And I agree with Piggot. The paper by Chau is about on option in
 g_order.


>>> Yes, and if memory serves (been a while since I used the program, so
>>> perhaps I am confusing something), this is what -o provides you so I
>>> thought it was relevant.  -od gives you the deuterium order parameters.
>>> The documentation for gmx order is indeed very sparse.
>>>
>>> Anyway, a general question:
 Can we expect to find a published article for each/some module(s) in
 Gromacs?

>>>
>>> No.  Many of the tools are just implementations of simple algorithms
>>> used widely in simulations.  Some do have specific references and those are
>>> generally printed to the screen output in bold blocks of text.
>>>
>>> With regards to deuterium order parameters, there is a well accepted and
>>> ubiquitously used equation, which Tom posted.
>>>
>>> I mean how/where can we figure out the underlying algorithm and
 comprehensive description of each analysis tool?


>>> That's why GROMACS is open source :)  Efforts are certainly always made
>>> to provide references when possible.
>>>
>>> -Justin
>>>
>>> Cheers
 Mohsen


 On Thu, Feb 23, 2017 at 10:06 AM, Mohsen Ramezanpour <
 ramezanpour.moh...@gmail.com> wrote:

 Hi Justin, Piggot,
>
> Thanks for your replies.
> I agree with that. The problem is that the situation is straightforward
> for bilayers as bilayers are usually in specific angles regarding the
> magnetic field (e.g. they are perpendicular, as it is the case in
> Vermeer study.)
> For example the normal to the bilayer is z and we do not need be worry
> about 

[gmx-users] Fwd: LINCS WARNING during EPM2 CO2 Energy Min

[Pimo Oni]

Dear community members,

Recently I'm using GMX 5.1.4 to simulate EPM2 CO2 with virtual sites, while
I met continual LINCS WARNING. I've been struggling for more than week but
make no progress in fixing it.. : (

Here attach my pdb, top, and mdp files below.
I would much appreciate any tip & comments.

Thanks
Pimo

-

***command used***

gmx_d insert-molecules -f co2EPM2.pdb -ci co2EPM2.pdb -o testco2.pdb -box 5
5 5 -nmol 999

gmx_d grompp -f em.mdp -po testco2em.mdp -c testco2.pdb -p co2EPM2.top -o
testco2em.tpr

gmx_d mdrun -s testco2em.tpr -deffnm testco2em

***error***
Step 12, time 0.012 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.00, max 0.00 (between atoms 2201 and 2202)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
 21 22   48.50.1978   0.1978  0.1978
   2496   2497   47.70.1978   0.1978  0.1978
   2496   2497   47.70.1978   0.1978  0.1978
   2496   2497   47.70.1978   0.1978  0.1978
   2496   2497   47.70.1978   0.1978  0.1978

***co2EPM2.pdb***
TITLE CO2 with dummy masses
REMARKTHIS IS A SIMULATION BOX
CRYST1   50.000   50.000   50.000  90.00  90.00  90.00 P 1   1
MODEL1
ATOM  1  M1  CO2 1   0.171   0.000   0.000  1.00  0.00

ATOM  2  M2  CO2 1   2.149   0.000   0.000  1.00  0.00

ATOM  3  C   CO2 1   1.160   0.000   0.000  1.00  0.00

ATOM  4  O1  CO2 1   0.000   0.000   0.000  1.00  0.00

ATOM  5  O2  CO2 1   2.320   0.000   0.000  1.00  0.00

TER
ENDMDL

***co2EPM2.top***
[ defaults ]
; nbfunc  comb-rule  gen-pairs  fudgeLJ  fudgeQQ
  1   2  no 1.0  1.0

 [ atomtypes ]
; type  mass charge  ptype sigma(nm) epsilon(kJ/M)
  M 22.00475  0. A 0.0   0.
  C  0.0  0.6512 V 0.27570   0.2339
  O  0.0 -0.3256 V 0.30330   0.6694


[ moleculetype ]
; name nrexcl
  CO2  2

[ atoms ]
; nr type resnr residu atom cgnr charge  mass
  1  M1 CO2M1   1 0. 22.00475
  2  M1 CO2M2   1 0. 22.00475
  3  C1 CO2C1 0.6512  0.0
  4  O1 CO2O1   1-0.3256  0.0
  5  O1 CO2O2   1-0.3256  0.0

[ constraints ]
; ai aj funct distance
  1  2  1 0.1978252

[ virtual_sites2 ]
; ai aj ak funct a
  3  1  2  1 0.5000
  4  1  2  1 1.086376
  5  2  1  1 1.086376

[ exclusions ]
3 4 5
4 5 3
5 4 3

[ system ]
CO2EPM2

[ molecules ]
; name nmol
  CO2  1000

***em.mdp***
define   =

; RUN CONTROL PARAMETERS
integrator   = steep
tinit= 0
dt   = 0.001
nsteps   = -1
init_step= 0
simulation_part  = 1
comm-mode= Linear
nstcomm  = 100
comm-grps=

emtol= 10.0
emstep   = 0.01
niter= 20
fcstep   = 0
nstcgsteep   = 1000
nbfgscorr= 10
energygrps   = system

cutoff-scheme= Verlet
nstlist  = 10
ns_type  = grid
pbc  = xyz
periodic_molecules   = no
verlet-buffer-tolerance  = -1
rlist= 1.5
rlistlong= -1
nstcalclr= -1

; Method for doing electrostatics
coulombtype  = PME
coulomb-modifier = Potential-shift-Verlet
rcoulomb-switch  = 0
rcoulomb = 1.5
; Relative dielectric constant for the medium and the reaction field
epsilon_r= 1
epsilon_rf   = 1
; Method for doing Van der Waals
vdw-type = Cut-off
vdw-modifier = Potential-shift-Verlet
; cut-off lengths
rvdw-switch  = 0
rvdw = 1.5
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = no
; Extension of the potential lookup tables beyond the cut-off
table-extension  = 1
; Separate tables between energy group pairs
energygrp-table  =
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
; EWALD/PME/PPPM parameters
pme_order= 4
ewald_rtol   = 1e-05
ewald-rtol-lj= 0.001
lj-pme-comb-rule = Geometric
ewald_geometry   = 3d
epsilon_surface  = 0

; Temperature coupling
tcoupl   = Berendsen
nsttcouple   = -1
nh-chain-length  = 10
print-nose-hoover-chain-variables = no
; Groups to couple separately
tc-grps  = System
; Time constant (ps) and reference temperature (K)
tau-t= 1
ref-t= 300
; pressure coupling
Pcoupl   = no

[gmx-users] LINCS WARNING during EPM2 CO2 Simulation

[Pimo Oni]

Dear community members,

Recently I'm using GMX 5.1.4 to simulate EPM2 CO2 with virtual sites, while
I met continual LINCS WARNING. I've been struggling for more than week but
make no progress in fixing it.. : (

Here attach my pdb, top, and mdp files below.
I would much appreciate any tip & comments.

Thanks
Pimo

-

***command used***

gmx_d insert-molecules -f co2EPM2.pdb -ci co2EPM2.pdb -o testco2.pdb -box 5
5 5 -nmol 999

gmx_d grompp -f em.mdp -po testco2em.mdp -c testco2.pdb -p co2EPM2.top -o
testco2em.tpr

gmx_d mdrun -s testco2em.tpr -deffnm testco2em

***error***
Step 12, time 0.012 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.00, max 0.00 (between atoms 2201 and 2202)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
 21 22   48.50.1978   0.1978  0.1978
   2496   2497   47.70.1978   0.1978  0.1978
   2496   2497   47.70.1978   0.1978  0.1978
   2496   2497   47.70.1978   0.1978  0.1978
   2496   2497   47.70.1978   0.1978  0.1978

***co2EPM2.pdb***
TITLE CO2 with dummy masses
REMARKTHIS IS A SIMULATION BOX
CRYST1   50.000   50.000   50.000  90.00  90.00  90.00 P 1   1
MODEL1
ATOM  1  M1  CO2 1   0.171   0.000   0.000  1.00  0.00

ATOM  2  M2  CO2 1   2.149   0.000   0.000  1.00  0.00

ATOM  3  C   CO2 1   1.160   0.000   0.000  1.00  0.00

ATOM  4  O1  CO2 1   0.000   0.000   0.000  1.00  0.00

ATOM  5  O2  CO2 1   2.320   0.000   0.000  1.00  0.00

TER
ENDMDL

***co2EPM2.top***
[ defaults ]
; nbfunc  comb-rule  gen-pairs  fudgeLJ  fudgeQQ
  1   2  no 1.0  1.0

 [ atomtypes ]
; type  mass charge  ptype sigma(nm) epsilon(kJ/M)
  M 22.00475  0. A 0.0   0.
  C  0.0  0.6512 V 0.27570   0.2339
  O  0.0 -0.3256 V 0.30330   0.6694


[ moleculetype ]
; name nrexcl
  CO2  2

[ atoms ]
; nr type resnr residu atom cgnr charge  mass
  1  M1 CO2M1   1 0. 22.00475
  2  M1 CO2M2   1 0. 22.00475
  3  C1 CO2C1 0.6512  0.0
  4  O1 CO2O1   1-0.3256  0.0
  5  O1 CO2O2   1-0.3256  0.0

[ constraints ]
; ai aj funct distance
  1  2  1 0.1978252

[ virtual_sites2 ]
; ai aj ak funct a
  3  1  2  1 0.5000
  4  1  2  1 1.086376
  5  2  1  1 1.086376

[ exclusions ]
3 4 5
4 5 3
5 4 3

[ system ]
CO2EPM2

[ molecules ]
; name nmol
  CO2  1000

***em.mdp***
define   =

; RUN CONTROL PARAMETERS
integrator   = steep
tinit= 0
dt   = 0.001
nsteps   = -1
init_step= 0
simulation_part  = 1
comm-mode= Linear
nstcomm  = 100
comm-grps=

emtol= 10.0
emstep   = 0.01
niter= 20
fcstep   = 0
nstcgsteep   = 1000
nbfgscorr= 10
energygrps   = system

cutoff-scheme= Verlet
nstlist  = 10
ns_type  = grid
pbc  = xyz
periodic_molecules   = no
verlet-buffer-tolerance  = -1
rlist= 1.5
rlistlong= -1
nstcalclr= -1

; Method for doing electrostatics
coulombtype  = PME
coulomb-modifier = Potential-shift-Verlet
rcoulomb-switch  = 0
rcoulomb = 1.5
; Relative dielectric constant for the medium and the reaction field
epsilon_r= 1
epsilon_rf   = 1
; Method for doing Van der Waals
vdw-type = Cut-off
vdw-modifier = Potential-shift-Verlet
; cut-off lengths
rvdw-switch  = 0
rvdw = 1.5
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = no
; Extension of the potential lookup tables beyond the cut-off
table-extension  = 1
; Separate tables between energy group pairs
energygrp-table  =
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
; EWALD/PME/PPPM parameters
pme_order= 4
ewald_rtol   = 1e-05
ewald-rtol-lj= 0.001
lj-pme-comb-rule = Geometric
ewald_geometry   = 3d
epsilon_surface  = 0

; Temperature coupling
tcoupl   = Berendsen
nsttcouple   = -1
nh-chain-length  = 10
print-nose-hoover-chain-variables = no
; Groups to couple separately
tc-grps  = System
; Time constant (ps) and reference temperature (K)
tau-t= 1
ref-t= 300
; pressure coupling
Pcoupl   = no

Re: [gmx-users] is there any special tutorial for the interaction of nanosheet and amino acids?

[Roja]

Oh my God,i face with wall at beginning as a BEGINNER ;)
I really appreciate you ,sir, for answering my questions patiently,I WILL BACK 
soon ;)

With regards
Rose

Sent from my iPhone

> On Oct 19, 2017, at 1:14, Alex  wrote:
> 
> No, what I am saying is that you need to meticulously modify the amber99
> forcefield (if that is indeed suitable) to represent your nanosheet. The
> charges have to come from appropriate sources, whether it's your Gaussian
> or whatever. This will fix all forcefield-related errors you are
> encountering. In order to learn about Gromacs forcefield format and how to
> do the editing, please consult the official Gromacs documentation. This
> really needs to be done before you start doing the xyz>pdb conversions, etc.
> 
> The "vacuum gap" is a moot point for MD simulations, especially ones
> involving solvent. Please understand the differences between DFT and
> particle-based simulations. You can put your nanosheet in a bunch of
> different boxes of appropriate size. This forum isn't the right place for
> asking this, I am only replying, because I have experience with using
> Gromacs for things it was never intended. :)
> 
> Best of luck!
> 
> Alex
> 
>> On Wed, Oct 18, 2017 at 3:14 PM, Rose  wrote:
>> 
>> Oh,you mean that i should make My sheet then just optimize it(with out
>> putting charge) and then convert it to .pdb file and use it in MD as an
>> input? I have checked the literature the suitable FF was amber99.
>> Different question;) , what is the difference between using vaccum gap
>> (that Will be implemented in structure.xyz file) and using smaller box
>> with periodic boundry condition(with out using vaccum gap),are they related
>> to each other at all?!!!
>> Sorry for these childish questions,but I really get confused.
>> 
>> With regards
>> Roja
>> 
>> 
>>> On Oct 19, 2017, at 0:08, Alex  wrote:
>>> 
>>> Hi Rose,
>>> 
>>> It sounds like a lot of things packed in a very short message, so let me
>>> try to clarify a few points:
>>> 
>>> 1. Gromacs is not DFT, it is particle-based. You simulated your nanosheet
>>> in Gaussian and it is my understanding that you used CHELPG to obtain the
>>> partial atomic charges.
>>> 
>>> 2. Those charges in general are not compatible with most MD forcefields
>>> implemented in Gromacs. If I remember correctly, AMBER is the closest to
>>> using CHELPG charges. So, my point is that you need to choose the MD
>>> forcefield properly and set the charges (all non-bonded parameters,
>> really)
>>> accordingly. The same goes for the bonded parameters to represent the
>>> nanomechanical properties of the sheet. This is beyond the scope of this
>>> discussion, as you definitely need to do a thorough literature search and
>>> see what forcefield is appropriate.
>>> 
>>> 3. You ask if your nanosheet is "suitable." Any structure is "suitable"
>> in
>>> principle, as long as the interactions are set properly.
>>> 
>>> It is hard to give any advice beyond that. Simulation of "custom"
>>> structures is a lot of effort. If your system of interest is small, an
>>> alternative to all of this could be DFTMD simulations using CP2K package.
>>> 
>>> Alex
>>> 
 On Wed, Oct 18, 2017 at 1:50 PM, rose rahmani 
>> wrote:
 
 first thank you for your attntion, i made ZnS nanosheet with VNL
 software,it has 33 atoms,i choosed vaccum gap,then i optimized and
>> charged
 it with gaussian03,the amino acid is threonin,for the first time i want
>> to
 study the interaction of these two structures, i am not even sure that
>> my
 nano sheet is suitable for this simulation or not,but for the as a
 beginning i prfeer to test it.
 
 
 
> On Wed, Oct 18, 2017 at 10:48 PM, Alex  wrote:
> 
> Hi,
> 
> That would probably depend on the nanosheet material, the particular
 amino
> acid, the solvent & ionic strength, temperature, etc, etc. But no,
>> there
 is
> no tutorial and yes, a "nanosheet" can be viewed as a ligand. :)
> 
> I don't know if this helps, but could you please first give us an idea
>> of
> what you're trying to do?
> 
> Alex
> 
> 
>> On 10/18/2017 1:09 PM, rose rahmani wrote:
>> 
>> Hi
>> 
>> I am a beginner user of GROMACS, i want to simulate the interaction of
>> nano
>> sheet with amino acid ,but i dont know what should do, how should i
 behave
>> with these structures ? is there any tutoroial for interaction of nano
>> sheet and amino acids?
>> is it like protein-ligand tutorial in GROMACS tutorial?
>> 
>> with regards
>> 
>> Rose
> 
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> * Please search the archive at http://www.gromacs.org/Support
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Re: [gmx-users] is there any special tutorial for the interaction of nanosheet and amino acids?

[Alex]

No, what I am saying is that you need to meticulously modify the amber99
forcefield (if that is indeed suitable) to represent your nanosheet. The
charges have to come from appropriate sources, whether it's your Gaussian
or whatever. This will fix all forcefield-related errors you are
encountering. In order to learn about Gromacs forcefield format and how to
do the editing, please consult the official Gromacs documentation. This
really needs to be done before you start doing the xyz>pdb conversions, etc.

The "vacuum gap" is a moot point for MD simulations, especially ones
involving solvent. Please understand the differences between DFT and
particle-based simulations. You can put your nanosheet in a bunch of
different boxes of appropriate size. This forum isn't the right place for
asking this, I am only replying, because I have experience with using
Gromacs for things it was never intended. :)

Best of luck!

Alex

On Wed, Oct 18, 2017 at 3:14 PM, Rose  wrote:

> Oh,you mean that i should make My sheet then just optimize it(with out
> putting charge) and then convert it to .pdb file and use it in MD as an
> input? I have checked the literature the suitable FF was amber99.
> Different question;) , what is the difference between using vaccum gap
> (that Will be implemented in structure.xyz file) and using smaller box
> with periodic boundry condition(with out using vaccum gap),are they related
> to each other at all?!!!
> Sorry for these childish questions,but I really get confused.
>
> With regards
> Roja
>
>
> > On Oct 19, 2017, at 0:08, Alex  wrote:
> >
> > Hi Rose,
> >
> > It sounds like a lot of things packed in a very short message, so let me
> > try to clarify a few points:
> >
> > 1. Gromacs is not DFT, it is particle-based. You simulated your nanosheet
> > in Gaussian and it is my understanding that you used CHELPG to obtain the
> > partial atomic charges.
> >
> > 2. Those charges in general are not compatible with most MD forcefields
> > implemented in Gromacs. If I remember correctly, AMBER is the closest to
> > using CHELPG charges. So, my point is that you need to choose the MD
> > forcefield properly and set the charges (all non-bonded parameters,
> really)
> > accordingly. The same goes for the bonded parameters to represent the
> > nanomechanical properties of the sheet. This is beyond the scope of this
> > discussion, as you definitely need to do a thorough literature search and
> > see what forcefield is appropriate.
> >
> > 3. You ask if your nanosheet is "suitable." Any structure is "suitable"
> in
> > principle, as long as the interactions are set properly.
> >
> > It is hard to give any advice beyond that. Simulation of "custom"
> > structures is a lot of effort. If your system of interest is small, an
> > alternative to all of this could be DFTMD simulations using CP2K package.
> >
> > Alex
> >
> >> On Wed, Oct 18, 2017 at 1:50 PM, rose rahmani 
> wrote:
> >>
> >> first thank you for your attntion, i made ZnS nanosheet with VNL
> >> software,it has 33 atoms,i choosed vaccum gap,then i optimized and
> charged
> >> it with gaussian03,the amino acid is threonin,for the first time i want
> to
> >> study the interaction of these two structures, i am not even sure that
> my
> >> nano sheet is suitable for this simulation or not,but for the as a
> >> beginning i prfeer to test it.
> >>
> >>
> >>
> >>> On Wed, Oct 18, 2017 at 10:48 PM, Alex  wrote:
> >>>
> >>> Hi,
> >>>
> >>> That would probably depend on the nanosheet material, the particular
> >> amino
> >>> acid, the solvent & ionic strength, temperature, etc, etc. But no,
> there
> >> is
> >>> no tutorial and yes, a "nanosheet" can be viewed as a ligand. :)
> >>>
> >>> I don't know if this helps, but could you please first give us an idea
> of
> >>> what you're trying to do?
> >>>
> >>> Alex
> >>>
> >>>
>  On 10/18/2017 1:09 PM, rose rahmani wrote:
> 
>  Hi
> 
>  I am a beginner user of GROMACS, i want to simulate the interaction of
>  nano
>  sheet with amino acid ,but i dont know what should do, how should i
> >> behave
>  with these structures ? is there any tutoroial for interaction of nano
>  sheet and amino acids?
>  is it like protein-ligand tutorial in GROMACS tutorial?
> 
>  with regards
> 
>  Rose
> >>>
> >>> --
> >>> 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!
> >>
> >> * 

Re: [gmx-users] (no subject)

[Dallas Warren]

Essential Dynamics = extracts the correlated motions of proteins to
understand the motions that are most fundamental to the activity of
the protein (http://www.gromacs.org/Documentation/How-tos/Essential_Dynamics)
Accelerated MD = enhanced-sampling method that improves the
conformational space sampling by reducing energy barriers separating
different states of a system
(http://www.ks.uiuc.edu/Research/namd/2.9/ug/node63.html)

Found via a quick search.

>From those quick definitions, they do two different things.
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 17 October 2017 at 21:16, Kingsley Theras Primus Dass .
<105726...@gms.tcu.edu.tw> wrote:
> Hi all,
> I have a very basic question about essential dynamics. I want to know
> whether essential dynamics function is similar to Accelerated MD ? Or
> essential dynamics is different from Accelerated MD ?
>
> Thanks in advance.
>
> Kingsleg Theras
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Re: [gmx-users] is there any special tutorial for the interaction of nanosheet and amino acids?

[Justin Lemkul]

On 10/18/17 5:14 PM, Rose wrote:

Oh,you mean that i should make My sheet then just optimize it(with out putting 
charge) and then convert it to .pdb file and use it in MD as an input? I have 
checked the literature the suitable FF was amber99.


What Alex is saying is that none of the force fields provided with 
GROMACS has knowledge of ZnS species and you will have to provide all of 
the parameters yourself. If they exist in the literature, then you need 
to implement them. If not, you need to parametrize it from scratch - a 
very advanced and difficult task (if it can even be made to work with a 
classical, pairwise additive functional form). A PDB file without a 
corresponding topology is useless.


-Justin


Different question;) , what is the difference between using vaccum gap (that 
Will be implemented in structure.xyz file) and using smaller box with periodic 
boundry condition(with out using vaccum gap),are they related to each other at 
all?!!!
Sorry for these childish questions,but I really get confused.

With regards
Roja



On Oct 19, 2017, at 0:08, Alex  wrote:

Hi Rose,

It sounds like a lot of things packed in a very short message, so let me
try to clarify a few points:

1. Gromacs is not DFT, it is particle-based. You simulated your nanosheet
in Gaussian and it is my understanding that you used CHELPG to obtain the
partial atomic charges.

2. Those charges in general are not compatible with most MD forcefields
implemented in Gromacs. If I remember correctly, AMBER is the closest to
using CHELPG charges. So, my point is that you need to choose the MD
forcefield properly and set the charges (all non-bonded parameters, really)
accordingly. The same goes for the bonded parameters to represent the
nanomechanical properties of the sheet. This is beyond the scope of this
discussion, as you definitely need to do a thorough literature search and
see what forcefield is appropriate.

3. You ask if your nanosheet is "suitable." Any structure is "suitable" in
principle, as long as the interactions are set properly.

It is hard to give any advice beyond that. Simulation of "custom"
structures is a lot of effort. If your system of interest is small, an
alternative to all of this could be DFTMD simulations using CP2K package.

Alex


On Wed, Oct 18, 2017 at 1:50 PM, rose rahmani  wrote:

first thank you for your attntion, i made ZnS nanosheet with VNL
software,it has 33 atoms,i choosed vaccum gap,then i optimized and charged
it with gaussian03,the amino acid is threonin,for the first time i want to
study the interaction of these two structures, i am not even sure that my
nano sheet is suitable for this simulation or not,but for the as a
beginning i prfeer to test it.




On Wed, Oct 18, 2017 at 10:48 PM, Alex  wrote:

Hi,

That would probably depend on the nanosheet material, the particular

amino

acid, the solvent & ionic strength, temperature, etc, etc. But no, there

is

no tutorial and yes, a "nanosheet" can be viewed as a ligand. :)

I don't know if this helps, but could you please first give us an idea of
what you're trying to do?

Alex



On 10/18/2017 1:09 PM, rose rahmani wrote:

Hi

I am a beginner user of GROMACS, i want to simulate the interaction of
nano
sheet with amino acid ,but i dont know what should do, how should i

behave

with these structures ? is there any tutoroial for interaction of nano
sheet and amino acids?
is it like protein-ligand tutorial in GROMACS tutorial?

with regards

Rose

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--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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* 

Re: [gmx-users] is there any special tutorial for the interaction of nanosheet and amino acids?

[Rose]

When I use amber99 FF i face error which says: residue NA is not identified in 
force field database!
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Re: [gmx-users] is there any special tutorial for the interaction of nanosheet and amino acids?

[Rose]

Oh,you mean that i should make My sheet then just optimize it(with out putting 
charge) and then convert it to .pdb file and use it in MD as an input? I have 
checked the literature the suitable FF was amber99.
Different question;) , what is the difference between using vaccum gap (that 
Will be implemented in structure.xyz file) and using smaller box with periodic 
boundry condition(with out using vaccum gap),are they related to each other at 
all?!!!
Sorry for these childish questions,but I really get confused.

With regards
Roja


> On Oct 19, 2017, at 0:08, Alex  wrote:
> 
> Hi Rose,
> 
> It sounds like a lot of things packed in a very short message, so let me
> try to clarify a few points:
> 
> 1. Gromacs is not DFT, it is particle-based. You simulated your nanosheet
> in Gaussian and it is my understanding that you used CHELPG to obtain the
> partial atomic charges.
> 
> 2. Those charges in general are not compatible with most MD forcefields
> implemented in Gromacs. If I remember correctly, AMBER is the closest to
> using CHELPG charges. So, my point is that you need to choose the MD
> forcefield properly and set the charges (all non-bonded parameters, really)
> accordingly. The same goes for the bonded parameters to represent the
> nanomechanical properties of the sheet. This is beyond the scope of this
> discussion, as you definitely need to do a thorough literature search and
> see what forcefield is appropriate.
> 
> 3. You ask if your nanosheet is "suitable." Any structure is "suitable" in
> principle, as long as the interactions are set properly.
> 
> It is hard to give any advice beyond that. Simulation of "custom"
> structures is a lot of effort. If your system of interest is small, an
> alternative to all of this could be DFTMD simulations using CP2K package.
> 
> Alex
> 
>> On Wed, Oct 18, 2017 at 1:50 PM, rose rahmani  wrote:
>> 
>> first thank you for your attntion, i made ZnS nanosheet with VNL
>> software,it has 33 atoms,i choosed vaccum gap,then i optimized and charged
>> it with gaussian03,the amino acid is threonin,for the first time i want to
>> study the interaction of these two structures, i am not even sure that my
>> nano sheet is suitable for this simulation or not,but for the as a
>> beginning i prfeer to test it.
>> 
>> 
>> 
>>> On Wed, Oct 18, 2017 at 10:48 PM, Alex  wrote:
>>> 
>>> Hi,
>>> 
>>> That would probably depend on the nanosheet material, the particular
>> amino
>>> acid, the solvent & ionic strength, temperature, etc, etc. But no, there
>> is
>>> no tutorial and yes, a "nanosheet" can be viewed as a ligand. :)
>>> 
>>> I don't know if this helps, but could you please first give us an idea of
>>> what you're trying to do?
>>> 
>>> Alex
>>> 
>>> 
 On 10/18/2017 1:09 PM, rose rahmani wrote:
 
 Hi
 
 I am a beginner user of GROMACS, i want to simulate the interaction of
 nano
 sheet with amino acid ,but i dont know what should do, how should i
>> behave
 with these structures ? is there any tutoroial for interaction of nano
 sheet and amino acids?
 is it like protein-ligand tutorial in GROMACS tutorial?
 
 with regards
 
 Rose
>>> 
>>> --
>>> 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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Re: [gmx-users] is there any special tutorial for the interaction of nanosheet and amino acids?

[Alex]

Hi Rose,

It sounds like a lot of things packed in a very short message, so let me
try to clarify a few points:

1. Gromacs is not DFT, it is particle-based. You simulated your nanosheet
in Gaussian and it is my understanding that you used CHELPG to obtain the
partial atomic charges.

2. Those charges in general are not compatible with most MD forcefields
implemented in Gromacs. If I remember correctly, AMBER is the closest to
using CHELPG charges. So, my point is that you need to choose the MD
forcefield properly and set the charges (all non-bonded parameters, really)
accordingly. The same goes for the bonded parameters to represent the
nanomechanical properties of the sheet. This is beyond the scope of this
discussion, as you definitely need to do a thorough literature search and
see what forcefield is appropriate.

3. You ask if your nanosheet is "suitable." Any structure is "suitable" in
principle, as long as the interactions are set properly.

It is hard to give any advice beyond that. Simulation of "custom"
structures is a lot of effort. If your system of interest is small, an
alternative to all of this could be DFTMD simulations using CP2K package.

Alex

On Wed, Oct 18, 2017 at 1:50 PM, rose rahmani  wrote:

> first thank you for your attntion, i made ZnS nanosheet with VNL
> software,it has 33 atoms,i choosed vaccum gap,then i optimized and charged
> it with gaussian03,the amino acid is threonin,for the first time i want to
> study the interaction of these two structures, i am not even sure that my
> nano sheet is suitable for this simulation or not,but for the as a
> beginning i prfeer to test it.
>
>
>
> On Wed, Oct 18, 2017 at 10:48 PM, Alex  wrote:
>
> > Hi,
> >
> > That would probably depend on the nanosheet material, the particular
> amino
> > acid, the solvent & ionic strength, temperature, etc, etc. But no, there
> is
> > no tutorial and yes, a "nanosheet" can be viewed as a ligand. :)
> >
> > I don't know if this helps, but could you please first give us an idea of
> > what you're trying to do?
> >
> > Alex
> >
> >
> > On 10/18/2017 1:09 PM, rose rahmani wrote:
> >
> >> Hi
> >>
> >> I am a beginner user of GROMACS, i want to simulate the interaction of
> >> nano
> >> sheet with amino acid ,but i dont know what should do, how should i
> behave
> >> with these structures ? is there any tutoroial for interaction of nano
> >> sheet and amino acids?
> >> is it like protein-ligand tutorial in GROMACS tutorial?
> >>
> >> with regards
> >>
> >> Rose
> >>
> >
> > --
> > 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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> > 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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[gmx-users] elevation the temperature

[marzieh dehghan]

Hi
Dear all

I want to elevate the temperature of my simulation system with the rate of
1 K/ns, so I would like to know which parameter should be changed to
elevate the temperature from 300 up to 450 K?

thanks a lot
best wishes
-- 




*Marzieh DehghanPhD of BiochemistryInstitute of biochemistry and Biophysics
(IBB)University of Tehran, Tehran- Iran.*
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Re: [gmx-users] .XYZ file format to .gro format

[Dr. K N Naresh, Post-Doctoral Fellow, Biosciences, SSSIHL]

As Justin pointed out in GROMACS per se we can't convert .xyz to .gro file.

On 19-Oct-2017 1:32 AM, "Dr. K N Naresh, Post-Doctoral Fellow, Biosciences,
SSSIHL"  wrote:

I can think of an option

If it is a small molecule, .xyz can be converted to .pdb using 'OpenBabel'.
And .gro file can be generated for the .pdb using PRODRG server online. I
guess even directly using the .xyz file, PRODRG can generate .gro file.

Best

Naresh

On 18-Oct-2017 8:53 PM, "Justin Lemkul"  wrote:

>
>
> On 10/18/17 11:01 AM, Nagasree Garapati wrote:
>
>> Hi
>>
>> I have structure of a molecule in .xyz format, is there an option similar
>> to pdb2gmx in gromacs to convert .xyz file to .gro files?
>>
>> Format conversion is done with editconf or trjconv; the fact that one
> gets a coordinate file at the end of pdb2gmx is actually somewhat of a side
> effect of producing a topology. One should not view pdb2gmx as a format
> conversion tool.
>
> To answer your question though, no, GROMACS tools do not deal with XYZ
> coordinates, largely because different programs produce different files
> called XYZ and I don't know of a uniform convention for them. But both .pdb
> and .gro have fixed file formats that are very easy to write using your
> favorite scripting language (Perl, Python, etc).
>
> -Justin
>
> --
>
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
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Re: [gmx-users] .XYZ file format to .gro format

[Dr. K N Naresh, Post-Doctoral Fellow, Biosciences, SSSIHL]

I can think of an option

If it is a small molecule, .xyz can be converted to .pdb using 'OpenBabel'.
And .gro file can be generated for the .pdb using PRODRG server online. I
guess even directly using the .xyz file, PRODRG can generate .gro file.

Best

Naresh

On 18-Oct-2017 8:53 PM, "Justin Lemkul"  wrote:

>
>
> On 10/18/17 11:01 AM, Nagasree Garapati wrote:
>
>> Hi
>>
>> I have structure of a molecule in .xyz format, is there an option similar
>> to pdb2gmx in gromacs to convert .xyz file to .gro files?
>>
>> Format conversion is done with editconf or trjconv; the fact that one
> gets a coordinate file at the end of pdb2gmx is actually somewhat of a side
> effect of producing a topology. One should not view pdb2gmx as a format
> conversion tool.
>
> To answer your question though, no, GROMACS tools do not deal with XYZ
> coordinates, largely because different programs produce different files
> called XYZ and I don't know of a uniform convention for them. But both .pdb
> and .gro have fixed file formats that are very easy to write using your
> favorite scripting language (Perl, Python, etc).
>
> -Justin
>
> --
>
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> 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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Re: [gmx-users] is there any special tutorial for the interaction of nanosheet and amino acids?

[rose rahmani]

first thank you for your attntion, i made ZnS nanosheet with VNL
software,it has 33 atoms,i choosed vaccum gap,then i optimized and charged
it with gaussian03,the amino acid is threonin,for the first time i want to
study the interaction of these two structures, i am not even sure that my
nano sheet is suitable for this simulation or not,but as a beginning i
prefer to test it

On Wed, Oct 18, 2017 at 11:20 PM, rose rahmani 
wrote:

> first thank you for your attntion, i made ZnS nanosheet with VNL
> software,it has 33 atoms,i choosed vaccum gap,then i optimized and charged
> it with gaussian03,the amino acid is threonin,for the first time i want to
> study the interaction of these two structures, i am not even sure that my
> nano sheet is suitable for this simulation or not,but for the as a
> beginning i prfeer to test it.
>
>
>
> On Wed, Oct 18, 2017 at 10:48 PM, Alex  wrote:
>
>> Hi,
>>
>> That would probably depend on the nanosheet material, the particular
>> amino acid, the solvent & ionic strength, temperature, etc, etc. But no,
>> there is no tutorial and yes, a "nanosheet" can be viewed as a ligand. :)
>>
>> I don't know if this helps, but could you please first give us an idea of
>> what you're trying to do?
>>
>> Alex
>>
>>
>> On 10/18/2017 1:09 PM, rose rahmani wrote:
>>
>>> Hi
>>>
>>> I am a beginner user of GROMACS, i want to simulate the interaction of
>>> nano
>>> sheet with amino acid ,but i dont know what should do, how should i
>>> behave
>>> with these structures ? is there any tutoroial for interaction of nano
>>> sheet and amino acids?
>>> is it like protein-ligand tutorial in GROMACS tutorial?
>>>
>>> with regards
>>>
>>> Rose
>>>
>>
>> --
>> 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.
>>
>
>
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Re: [gmx-users] is there any special tutorial for the interaction of nanosheet and amino acids?

[rose rahmani]

first thank you for your attntion, i made ZnS nanosheet with VNL
software,it has 33 atoms,i choosed vaccum gap,then i optimized and charged
it with gaussian03,the amino acid is threonin,for the first time i want to
study the interaction of these two structures, i am not even sure that my
nano sheet is suitable for this simulation or not,but for the as a
beginning i prfeer to test it.



On Wed, Oct 18, 2017 at 10:48 PM, Alex  wrote:

> Hi,
>
> That would probably depend on the nanosheet material, the particular amino
> acid, the solvent & ionic strength, temperature, etc, etc. But no, there is
> no tutorial and yes, a "nanosheet" can be viewed as a ligand. :)
>
> I don't know if this helps, but could you please first give us an idea of
> what you're trying to do?
>
> Alex
>
>
> On 10/18/2017 1:09 PM, rose rahmani wrote:
>
>> Hi
>>
>> I am a beginner user of GROMACS, i want to simulate the interaction of
>> nano
>> sheet with amino acid ,but i dont know what should do, how should i behave
>> with these structures ? is there any tutoroial for interaction of nano
>> sheet and amino acids?
>> is it like protein-ligand tutorial in GROMACS tutorial?
>>
>> with regards
>>
>> Rose
>>
>
> --
> 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.
>
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Re: [gmx-users] is there any special tutorial for the interaction of nanosheet and amino acids?

[Alex]

Hi,

That would probably depend on the nanosheet material, the particular 
amino acid, the solvent & ionic strength, temperature, etc, etc. But no, 
there is no tutorial and yes, a "nanosheet" can be viewed as a ligand. :)


I don't know if this helps, but could you please first give us an idea 
of what you're trying to do?


Alex

On 10/18/2017 1:09 PM, rose rahmani wrote:

Hi

I am a beginner user of GROMACS, i want to simulate the interaction of nano
sheet with amino acid ,but i dont know what should do, how should i behave
with these structures ? is there any tutoroial for interaction of nano
sheet and amino acids?
is it like protein-ligand tutorial in GROMACS tutorial?

with regards

Rose


--
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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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mail to gmx-users-requ...@gromacs.org.

[gmx-users] is there any special tutorial for the interaction of nanosheet and amino acids?

[rose rahmani]

Hi

I am a beginner user of GROMACS, i want to simulate the interaction of nano
sheet with amino acid ,but i dont know what should do, how should i behave
with these structures ? is there any tutoroial for interaction of nano
sheet and amino acids?
is it like protein-ligand tutorial in GROMACS tutorial?

with regards

Rose
-- 
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Re: [gmx-users] .XYZ file format to .gro format

[Justin Lemkul]

On 10/18/17 11:01 AM, Nagasree Garapati wrote:

Hi

I have structure of a molecule in .xyz format, is there an option similar to 
pdb2gmx in gromacs to convert .xyz file to .gro files?

Format conversion is done with editconf or trjconv; the fact that one 
gets a coordinate file at the end of pdb2gmx is actually somewhat of a 
side effect of producing a topology. One should not view pdb2gmx as a 
format conversion tool.


To answer your question though, no, GROMACS tools do not deal with XYZ 
coordinates, largely because different programs produce different files 
called XYZ and I don't know of a uniform convention for them. But both 
.pdb and .gro have fixed file formats that are very easy to write using 
your favorite scripting language (Perl, Python, etc).


-Justin

--

==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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[gmx-users] .XYZ file format to .gro format

[Nagasree Garapati]

Hi

I have structure of a molecule in .xyz format, is there an option similar to 
pdb2gmx in gromacs to convert .xyz file to .gro files?


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Re: [gmx-users] Running MD simulations at a particular temperature

[Justin Lemkul]

On 10/18/17 9:41 AM, Dilip H N wrote:

Justin Sir,
Even i am also using Charmm 36FF. So as u have mentioned in previois
message, can u kindly suggest then what ate the correct cutoffs..??
And what would be the other modifications that needs to be done in order to
incorporate the Charmm FF


I think I post this link to the mailing list weekly...

http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM

-Justin


Thank you



 Sent with Mailtrack


On Wed, Oct 18, 2017 at 6:46 PM, Justin Lemkul  wrote:



On 10/18/17 9:14 AM, Pandya, Akash wrote:


So I equilibrated my system at 338.15 K , do I still need to use the
simulated annealing option to maintain that temperature? My NPT mdp file is
shown below.


Simply maintaining a temperature is done by employing a thermostat and
reference temperature. Annealing is used to change temperature over time,
so you don't need that here.

title   = CHARMM27 A33FabGLY NPT equilibration

define  = -DPOSRES  ; position restrain the protein
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 5 ; 2 * 5 = 100 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 100   ; save coordinates every 0.2 ps
nstvout = 100   ; save velocities every 0.2 ps
nstenergy   = 100   ; save energies every  0.2 ps
nstlog  = 100   ; update log file every 0.2 ps
; Bond parameters
continuation= yes   ; Restarting after NVT
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
ns_type = grid  ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist   = 1.0   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.0   ; short-range electrostatic cutoff (in nm)
rvdw= 1.0   ; short-range van der Waals cutoff (in nm)


Your title says CHARMM, but these aren't the correct cutoffs for using the
CHARMM force field.

-Justin


; 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  = Nose-Hoover   ; Nose-Hoover thermostat
tc-grps = Protein Non-Protein   ; two coupling groups - more
accurate
tau_t   = 0.5   0.5 ; time constant, in ps
ref_t   = 338.15338.15  ; reference temperature, one for
each group, in K
; Pressure coupling is on
pcoupl  = Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype  = isotropic ; uniform scaling of box vectors
tau_p   = 2.0   ; time constant, in ps
ref_p   = 1.0   ; reference pressure, in bar
compressibility = 4.5e-5; isothermal compressibility of water,
bar^-1
refcoord_scaling = com
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no; Velocity generation is off


Akash
-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 Mark
Abraham
Sent: 17 October 2017 10:28
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Running MD simulations at a particular
temperature

Hi,

That's your question as part of your experimental design. Why do you want
to do simulated annealing?

Mark

On Tue, Oct 17, 2017 at 10:57 AM Pandya, Akash 

Re: [gmx-users] Running MD simulations at a particular temperature

[Dilip H N]

Justin Sir,
Even i am also using Charmm 36FF. So as u have mentioned in previois
message, can u kindly suggest then what ate the correct cutoffs..??
And what would be the other modifications that needs to be done in order to
incorporate the Charmm FF

Thank you



 Sent with Mailtrack


On Wed, Oct 18, 2017 at 6:46 PM, Justin Lemkul  wrote:

>
>
> On 10/18/17 9:14 AM, Pandya, Akash wrote:
>
>> So I equilibrated my system at 338.15 K , do I still need to use the
>> simulated annealing option to maintain that temperature? My NPT mdp file is
>> shown below.
>>
>
> Simply maintaining a temperature is done by employing a thermostat and
> reference temperature. Annealing is used to change temperature over time,
> so you don't need that here.
>
> title   = CHARMM27 A33FabGLY NPT equilibration
>> define  = -DPOSRES  ; position restrain the protein
>> ; Run parameters
>> integrator  = md; leap-frog integrator
>> nsteps  = 5 ; 2 * 5 = 100 ps
>> dt  = 0.002 ; 2 fs
>> ; Output control
>> nstxout = 100   ; save coordinates every 0.2 ps
>> nstvout = 100   ; save velocities every 0.2 ps
>> nstenergy   = 100   ; save energies every  0.2 ps
>> nstlog  = 100   ; update log file every 0.2 ps
>> ; Bond parameters
>> continuation= yes   ; Restarting after NVT
>> 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
>> ns_type = grid  ; search neighboring grid cells
>> nstlist = 5 ; 10 fs
>> rlist   = 1.0   ; short-range neighborlist cutoff (in nm)
>> rcoulomb= 1.0   ; short-range electrostatic cutoff (in nm)
>> rvdw= 1.0   ; short-range van der Waals cutoff (in nm)
>>
>
> Your title says CHARMM, but these aren't the correct cutoffs for using the
> CHARMM force field.
>
> -Justin
>
>
> ; 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  = Nose-Hoover   ; Nose-Hoover thermostat
>> tc-grps = Protein Non-Protein   ; two coupling groups - more
>> accurate
>> tau_t   = 0.5   0.5 ; time constant, in ps
>> ref_t   = 338.15338.15  ; reference temperature, one for
>> each group, in K
>> ; Pressure coupling is on
>> pcoupl  = Parrinello-Rahman ; Pressure coupling on in NPT
>> pcoupltype  = isotropic ; uniform scaling of box vectors
>> tau_p   = 2.0   ; time constant, in ps
>> ref_p   = 1.0   ; reference pressure, in bar
>> compressibility = 4.5e-5; isothermal compressibility of water,
>> bar^-1
>> refcoord_scaling = com
>> ; Periodic boundary conditions
>> pbc = xyz   ; 3-D PBC
>> ; Dispersion correction
>> DispCorr= EnerPres  ; account for cut-off vdW scheme
>> ; Velocity generation
>> gen_vel = no; Velocity generation is off
>>
>>
>> Akash
>> -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 Mark
>> Abraham
>> Sent: 17 October 2017 10:28
>> To: gmx-us...@gromacs.org
>> Subject: Re: [gmx-users] Running MD simulations at a particular
>> temperature
>>
>> Hi,
>>
>> That's your question as part of your experimental design. Why do you want
>> to do simulated annealing?
>>
>> Mark
>>
>> On Tue, Oct 17, 2017 at 10:57 AM Pandya, Akash > >
>> wrote:
>>
>> Is simulated annealing carried out during NPT or in the production run?
>>>
>>> Akash
>>>
>>> -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 Justin
>>> Lemkul
>>> Sent: 20 September 2017 03:20
>>> To: gmx-us...@gromacs.org
>>> Subject: Re: [gmx-users] Running MD simulations at a particular
>>> temperature
>>>
>>>
>>>
>>> On 9/19/17 4:25 PM, Pandya, Akash wrote:
>>>
 Hi all,

 I want to run my MD simulation at 65 degrees Celsius. The mdp file
 has a

>>> field as shown below:
>>>
 ref_t= 338.15  338.15 ; reference

>>> temperature, one for each group, in K
>>>
 I am wondering whether the simulation has already reached the
 desired

>>> 

Re: [gmx-users] Running MD simulations at a particular temperature

[Justin Lemkul]

On 10/18/17 9:14 AM, Pandya, Akash wrote:

So I equilibrated my system at 338.15 K , do I still need to use the simulated 
annealing option to maintain that temperature? My NPT mdp file is shown below.


Simply maintaining a temperature is done by employing a thermostat and 
reference temperature. Annealing is used to change temperature over 
time, so you don't need that here.



title   = CHARMM27 A33FabGLY NPT equilibration
define  = -DPOSRES  ; position restrain the protein
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 5 ; 2 * 5 = 100 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 100   ; save coordinates every 0.2 ps
nstvout = 100   ; save velocities every 0.2 ps
nstenergy   = 100   ; save energies every  0.2 ps
nstlog  = 100   ; update log file every 0.2 ps
; Bond parameters
continuation= yes   ; Restarting after NVT
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
ns_type = grid  ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist   = 1.0   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.0   ; short-range electrostatic cutoff (in nm)
rvdw= 1.0   ; short-range van der Waals cutoff (in nm)


Your title says CHARMM, but these aren't the correct cutoffs for using 
the CHARMM force field.


-Justin


; 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  = Nose-Hoover   ; Nose-Hoover thermostat
tc-grps = Protein Non-Protein   ; two coupling groups - more accurate
tau_t   = 0.5   0.5 ; time constant, in ps
ref_t   = 338.15338.15  ; reference temperature, one for each 
group, in K
; Pressure coupling is on
pcoupl  = Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype  = isotropic ; uniform scaling of box vectors
tau_p   = 2.0   ; time constant, in ps
ref_p   = 1.0   ; reference pressure, in bar
compressibility = 4.5e-5; isothermal compressibility of water, bar^-1
refcoord_scaling = com
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no; Velocity generation is off


Akash
-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 Mark 
Abraham
Sent: 17 October 2017 10:28
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Running MD simulations at a particular temperature

Hi,

That's your question as part of your experimental design. Why do you want to do 
simulated annealing?

Mark

On Tue, Oct 17, 2017 at 10:57 AM Pandya, Akash 
wrote:


Is simulated annealing carried out during NPT or in the production run?

Akash

-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 Justin
Lemkul
Sent: 20 September 2017 03:20
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Running MD simulations at a particular
temperature



On 9/19/17 4:25 PM, Pandya, Akash wrote:

Hi all,

I want to run my MD simulation at 65 degrees Celsius. The mdp file
has a

field as shown below:

ref_t= 338.15  338.15 ; reference

temperature, one for each group, in K

I am wondering whether the simulation has already reached the
desired

temperature or does it heat up to 65 degrees throughout the course of
the simulation? I hope this makes sense.

The answer depends on what you're doing.  If you've set "gen-vel = yes"
and "gen-temp = 338.15" then you are initializing a simulation with
random velocities according to a Maxwell distribution at that
temperature. If your system is at some other temperature and you're
just trying to use a thermostat to force a change in that temperature, there's no real 
"warming"
going on, rather the thermostat is going to push the velocity
distribution towards the desired temperature.  Warming a system is
done via simulated annealing options.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129

Re: [gmx-users] Running MD simulations at a particular temperature

[Pandya, Akash]

So I equilibrated my system at 338.15 K , do I still need to use the simulated 
annealing option to maintain that temperature? My NPT mdp file is shown below.

title   = CHARMM27 A33FabGLY NPT equilibration 
define  = -DPOSRES  ; position restrain the protein
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 5 ; 2 * 5 = 100 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 100   ; save coordinates every 0.2 ps
nstvout = 100   ; save velocities every 0.2 ps
nstenergy   = 100   ; save energies every  0.2 ps
nstlog  = 100   ; update log file every 0.2 ps
; Bond parameters
continuation= yes   ; Restarting after NVT 
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
ns_type = grid  ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist   = 1.0   ; short-range neighborlist cutoff (in nm)
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  = Nose-Hoover   ; Nose-Hoover thermostat
tc-grps = Protein Non-Protein   ; two coupling groups - more accurate
tau_t   = 0.5   0.5 ; time constant, in ps
ref_t   = 338.15338.15  ; reference temperature, one for each 
group, in K
; Pressure coupling is on
pcoupl  = Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype  = isotropic ; uniform scaling of box vectors
tau_p   = 2.0   ; time constant, in ps
ref_p   = 1.0   ; reference pressure, in bar
compressibility = 4.5e-5; isothermal compressibility of water, bar^-1
refcoord_scaling = com
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no; Velocity generation is off


Akash 
-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 Mark 
Abraham
Sent: 17 October 2017 10:28
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Running MD simulations at a particular temperature

Hi,

That's your question as part of your experimental design. Why do you want to do 
simulated annealing?

Mark

On Tue, Oct 17, 2017 at 10:57 AM Pandya, Akash 
wrote:

> Is simulated annealing carried out during NPT or in the production run?
>
> Akash
>
> -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 Justin 
> Lemkul
> Sent: 20 September 2017 03:20
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Running MD simulations at a particular 
> temperature
>
>
>
> On 9/19/17 4:25 PM, Pandya, Akash wrote:
> > Hi all,
> >
> > I want to run my MD simulation at 65 degrees Celsius. The mdp file 
> > has a
> field as shown below:
> >
> > ref_t= 338.15  338.15 ; reference
> temperature, one for each group, in K
> >
> > I am wondering whether the simulation has already reached the 
> > desired
> temperature or does it heat up to 65 degrees throughout the course of 
> the simulation? I hope this makes sense.
>
> The answer depends on what you're doing.  If you've set "gen-vel = yes"
> and "gen-temp = 338.15" then you are initializing a simulation with 
> random velocities according to a Maxwell distribution at that 
> temperature. If your system is at some other temperature and you're 
> just trying to use a thermostat to force a change in that temperature, 
> there's no real "warming"
> going on, rather the thermostat is going to push the velocity 
> distribution towards the desired temperature.  Warming a system is 
> done via simulated annealing options.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> 

Re: [gmx-users] [gmx-developers] Fw: Fw: Two questions about PME-User in coulombtype

[Du, Yu]

Berk, thanks for your reply.

I have Cc this email including your answers to the GMX-User.

Regards, 

Yu

> -Original Messages-
> From: "Berk Hess" 
> Sent Time: 2017-10-18 19:56:30 (Wednesday)
> To: gmx-develop...@gromacs.org
> Cc: 
> Subject: Re: [gmx-developers] Fw: [gmx-users] Fw: Two questions about 
> PME-User in coulombtype
> 
> Hi,
> 
> I don't know if I can still mail to the gmx-users list (and I don't have 
> time to check now), so I answer to the devloper list, but please post my 
> answers below to the gmx-users list.
> 
> Cheers,
> 
> Berk
> 
> Answers:
> 
> 1) Correct.
> 2) Correct.
> 3) PME splits the Coulomb interaction into two parts and this splitting 
> depends on beta. All you need to know is that up to the cut-off 
> distance, you exactly get the interaction you set in the table. Beyond 
> the cut-off you get 1/r.
> 
> Your potential values should have 10 decimals to be sure that rounding 
> errors are negligible. In principle, also r should have 10 decimals, but 
> 0.002000 is identical to 0.002 (and 0.00 to 0.000 or 0).
> 
> On 2017-10-17 15:15, Du, Yu wrote:
> > Dear GMX Developers,
> >
> > I'm sorry for repeting sending this email to the mail list. I think the 
> > PME-User is not common for users to use and the related explanation is 
> > scarce.
> >
> > Hope you gurus can help me. Thanks a lot.
> >
> > Yu
> >
> >
> > -Original Messages-
> > From: "Du, Yu" 
> > Sent Time: 2017-10-15 17:17:14 (Sunday)
> > To: GMX-user 
> > Subject: [gmx-users] Two questions about PME-User in coulombtype
> >
> > Hi GMX Users,
> >
> >
> > I'm using tabulized potentials between energygrp-table = Protein Ligand. 
> > I'm writing to inquiring the details of PME-User parameter.
> >
> >
> > I have seen some discussions in the GMX User mail list and the explanation 
> > in user guide. I still can't ensure I have grasped the meaning of PME-User 
> > in coulombtype option. The following is my understanding. If anything is 
> > wrong please point out. Thanks a lot.
> >
> >
> > 1) Because the mesh part also contributes below the cut-off, the PME mesh 
> > contribution is subtracted from the user table by gmx mdrun to get the 
> > short-range coulombic interaction below the rcoulomb.
> >
> >
> > 2) The tabulized potential is short-range interaction. If I use 
> > coulombtype=User, I only have the short-range interaction defined in the 
> > tabulized potetial files and no PME between any components (i.e. Protein, 
> > Ligand, SOL, ions) in the system.
> >
> >
> > 3)If I use coulombtype=PME-User instead, I will get the short-range 
> > interaction defined in the tabulized potetial files and PME between any 
> > components (i.e. Protein, Ligand, SOL, ions) in the system like normal 
> > coulombtype=PME.
> >
> >
> > --Next Question--
> > "The PME mesh contribution is subtracted from the user table by gmx mdrun. 
> > Because of this subtraction the user tables should contain about 10 decimal 
> > places."
> >
> > The second question is how to deal with the PME-User's "10 decimal places" 
> > in user guide of the coulombtype option. Does it mean that the original 
> > step of r = 0.002 nm in mixed precision should be 0.0# nm? What 
> > should be the detailed step size of r?
> >
> >
> >
> 

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Re: [gmx-users] Does GROMACS supports ab initio molecular dynamics simulations?

[Justin Lemkul]

On 10/18/17 8:21 AM, lxj2586 wrote:

Dear GMX Users,
   
  I would like to simulate the interactions between graphene oxide sheets and cations, which needs to consider the electronic behavior. Therefore, I plan to use ab initio MD (AIMD) simulations. Could anyone tell me whether GROMACS can do AIMD?
   


It cannot. There is a QM/MM interface to QM codes, but it is not 
actively maintained and needs some work.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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[gmx-users] Does GROMACS supports ab initio molecular dynamics simulations?

[lxj2586]

Dear GMX Users,
  
 I would like to simulate the interactions between graphene oxide sheets and 
cations, which needs to consider the electronic behavior. Therefore, I plan to 
use ab initio MD (AIMD) simulations. Could anyone tell me whether GROMACS can 
do AIMD?
  
 Many thanks for your help!
  
 Xujun
  
 --  
   Xujun LIANG, PhD
 School of Environment
Jinan University
Guangzhou 511443
Guangdong Province
P.R. China
 

 Best wishes to you!!
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Re: [gmx-users] Regarding usage of version of CGenFF

[Justin Lemkul]

On 10/18/17 1:14 AM, Dilip H N wrote:

Hello,
I was able to generate .str file from CGenFF server, and after this, i am
able to convert the .str files into .itp, .prm  files etc., successfully by
using the cgennff_charmm2gmx.py script. but at the end, i am getting the
notes as:-

NOTE1: Code tested with python 2.7.3. Your version: 2.7.13 |Anaconda 4.4.0
(64-bit)| (default, Dec 20 2016, 23:09:15)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]

NOTE2: Please be sure to use the same version of CGenFF in your simulations
that was used during parameter generation:
--Version of CGenFF detected in ligand.str : 3.0.1
--Version of CGenFF detected in  charmm36-jul2017.ff/forcefield.doc: 4.0

WARNING: CGenFF versions are not equivalent!
So,
1] Does the versions make any significance here...?? is it ok if the
version i am using with acceptable...

2] And how to solve the version of CGenFF...?? my ligand.str is 3.0.1 and
the charmm36-jul2017.ff is 4.0 version...


Don't worry about this difference. The web server needs to be updated, 
but not in any way that affects the end user.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] Regarding non zwitterionic structure to zwitterionic structure while using gmxpdb2gmx

[Justin Lemkul]

On 10/18/17 6:05 AM, Dilip H N wrote:

Hello,
I have a neutral glycine molecule [NH2CH2COOH] and if i give gmx pdb2gmx i
m getting error as:-
Fatal error:
Atom HO in residue GLY 1 was not found in rtp entry GLY with 11 atoms
while sorting atoms.
For a hydrogen, this can be a different protonation state..

So i use the -ignh flag (gmx pdb2gmx gly.pdb -o gly.gro -ignh) which gives
me a zwitterionic structure and topology is created.(since i need to
simulate in water, the zwitterionic structure is good.)

1] But if i convert the zwitterionic form of glycine into .mol2 format and
upload to CGENFF server (i am using charmm FF) for creating the topology,
the .str file that is generated shows a penalty of 99.5, which is not good.

RESI glycin   0.000 ! param penalty=   0.100 ; charge penalty=  99.591
GROUP! CHARGE   CH_PENALTY
ATOM N  NG3P3  -0.336 !   32.195
ATOM H1 HGP20.330 !2.200
ATOM H2 HGP20.330 !2.200
ATOM H3 HGP20.330 !2.200
ATOM CA CG324   0.241 !   99.591
ATOM HA1HGA20.090 !3.821
ATOM HA2HGA20.090 !3.821
ATOM C  CG2O3   0.445 !   98.841
ATOM OT1OG2D2  -0.760 !8.256
ATOM OT2OG2D2  -0.760 !8.256

But if i compare the topology created by 'gmx pdb2gmx gly.pdb -o
gly.gro -ignh' command then the charges of the atoms are different...
then how is this possible..??


CGenFF parametrizes whatever it finds based on a set of rules, which 
come from relationships to other molecules. This is intrinsically 
different than the library of highly optimized residues already built 
into the force field.


DO NOT use CGenFF topologies for molecules that are already specifically 
tuned as part of the CHARMM force field. Use what pdb2gmx gives you.


-Justin


Which topology is more reliable..??

2] if non zwitterionic form of glycine is given in form of .mol2, then
the .str file give zero penalty.

RESI *0.000 ! param penalty=   0.000 ; charge penalty=   0.000
GROUP! CHARGE   CH_PENALTY
ATOM N  NG321  -0.956 !0.000
ATOM CA CG321   0.100 !0.000
ATOM C  CG2O2   0.751 !0.000
ATOM O  OG2D1  -0.551 !0.000
ATOM HA1HGA20.090 !0.000
ATOM HA2HGA20.090 !0.000
ATOM H  HGPAM2  0.338 !0.000
ATOM HN HGPAM2  0.338 !0.000
ATOM OXTOG311  -0.629 !0.000
ATOM HO HGP10.429 !0.000

So which topology is more reliable for simulations..??

Any suggestions ar appreciated..



--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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