date:20120509

On 5/9/12 11:59 AM, Faezeh Kargar wrote:

Dear all,

my coarse grained simulations contain a cubic box with 16 peptides. After 85ns
peptides aggregate but because of PBC I have problem in analyzing some data like
radius of gyration and clustering. I searched mailing list to solve this problem
by trjconv. I examined its different options but without any results. casually
genconf came in my mind. I want to use this command for a trajectory with option
-trj

genconf -f .tpr -trj .xtc/.gro -o .gro -nbox 2 1 1

but when I use it I face with "Segmentation fault". I searched mailing list and
found just one
question"http://lists.gromacs.org/pipermail/gmx-users/2004-July/011196.html";
whithout answer.

It's almost certainly a bug, but the fact that no one has asked about the -trj
option in nearly eight years suggests it's probably not a high priority to fix,
or simply that no one ever noticed it. In any case, genconf is not likely to be
a suitable solution.

Please guide me wheather this command can help me to generate an aggregated
system for analyzing? If Yes, How? If No help me please?

You need trjconv, and likely several instances of it. Complex systems like
these require great care and potentially custom index groups. There is a
generic trjconv workflow here:

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow

There are also numerous posts in the list archive regarding clustering of
various molecules, including peptides and micelles. The tips there will likely
guide you, but if you need further help you'll need to provide explicit commands
that you've tried, what they produced, and why it's not what you're after. The
solution is in trjconv, but without knowing what you've tried, it's hard to
provide additional help.

-Justin

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.

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

[gmx-users] genconf -trj?!?

2012-05-09 Thread Faezeh Kargar






Dear all,
my coarse grained simulations contain a cubic box
with 16 peptides. After 85ns peptides aggregate but because of PBC I
have problem in analyzing some data like radius of gyration and
clustering. I searched mailing list to solve this problem by trjconv. I
examined its different options but without any results. casually
genconf came in my mind. I want to use this command for a trajectory
with option -trj
genconf -f .tpr -trj .xtc/.gro -o .gro -nbox 2 1
1
 but when I use it I face with "Segmentation
fault". I searched mailing list and found just one
question"http://lists.gromacs.org/pipermail/gmx-users/2004-July/011196.html";
whithout answer.


Please guide me wheather this command can help me to generate an
aggregated system for analyzing? If Yes, How? If No help me
please?Thank you in advance

Faezeh Kargar



-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.

-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Restraining atoms




On 5/9/12 11:34 AM, Steven Neumann wrote:

Dear Gmx Users,

My plane surface is made of atoms. I would like to restrain positions between
them so they will move all togehter or create bonds between them. Would you
advise how to do this in the easiest way?



If you need to "restrain positions" then you need [position_restraints].  The 
form of the restraints follows from the structure of the topology.


Also note that you cannot create bonds in a classical MD simulation.  If you 
need to maintain some distances, then use actual bonds or [distance_restraints].


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

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

[gmx-users] Restraining atoms

Dear Gmx Users,

My plane surface is made of atoms. I would like to restrain positions
between them so they will move all togehter or create bonds between them.
Would you advise how to do this in the easiest way?

Steven
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Charge derrivation for OPLSAA forcefield

2012-05-09 Thread Dommert Florian

On Tue, 2012-05-08 at 11:38 -0700, Milinda Samaraweera wrote: 
> Hi Guys
> 
> 
> I was using the program http://q4md-forcefieldtools.org/RED/ to
> derrive ESP based charges for some molecules that I study. Is this a
> correct method to do so if not please let me know what are the other
> methods that are available.
> 

Hi,

this is really a hard questions to answer. Different methods to derive
partial charges are present, which rely on various ideas. Actually, the
partial charges of a force field should be consistent, because they are
anyway just an approximation for the true charge density. Common force
fields like AMBER or OPLS-AA were constructed with different
consideration, giving rise to the differences, though they allow to
desribe the same molecules. So I would study, how the remaining
parameters of the applied force field were derived. Furthermore be aware
that altering a single charge of force field might require readaption of
dihedral and LJ parameters. Hence, always be careful and benchmark the
force field  against single as well collective static and dynamic
properties, carefully.

/Flo

> 
> thanks alot
>  
> Milinda Samaraweera
> University of Connecticut
> Department of Chemistry
> 55 N Eagleville road
> unit 3060
> Storrs CT
> USA
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

-- 
Florian Dommert
Dipl. - Phys.

Institute for Computational Physics
University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

EMail: domm...@icp.uni-stuttgart.de
Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert

Tel.: +49 - (0)711 - 68563613
Fax.: +49 - (0)711 - 68563658

signature.asc
Description: This is a digitally signed message part
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Test Particle Insertion of Water

Thank you! I have missed it somehow. I can still use my xtc trajectory.

Steven

On Wed, May 9, 2012 at 3:16 PM, Javier Cerezo  wrote:

>  The trr file has something wrong. Look at "Coords", it has 0 frames
>
> You may have forgotten to set nstxout to a non-zero value?
>
> Javier
>
> El 09/05/12 16:10, Steven Neumann escribió:
>
> I added one water molecule in my topology to all water molecules:
>
> [ molecules ]
> ; Compound#mols
> Alanine40
> SOL   724
>
> Maybe I should add aditional line like:
>
> [ molecules ]
> ; Compound#mols
> Alanine40
> SOL   723
> SOL  1
>
> What do you think?
>
>
> On Wed, May 9, 2012 at 3:04 PM, Steven Neumann wrote:
>
>> Checking file md.trr
>> trn version: GMX_trn_file (single precision)
>> Reading frame   0 time0.000
>> # Atoms  2569
>> Last frame   2000 time 10.000
>>
>>
>> Item#frames Timestep (ps)
>> Step  200150
>> Time  200150
>> Lambda200150
>> Coords   0
>> Velocities200150
>> Forces   0
>> Box   200150
>>
>> Well, it looks ok. Any suggestions?
>>
>>
>>  On Wed, May 9, 2012 at 3:01 PM, Javier Cerezo  wrote:
>>
>>>  Sorry, I saw now the command line you've posted. Did you check your trr
>>> with gmxcheck?
>>>
>>>
>>> El 09/05/12 15:49, Steven Neumann escribió:
>>>
>>> hello gmx users,
>>>
>>>
>>> I am sorry for bothering you but I was searching mailing list and no
>>> results. I have a problem with my test particle insertion as I run the
>>> workflow I described previously with my mdp:
>>>
>>> title   = Test Particle Insertion
>>> ; Run parameters
>>> integrator  = tpi
>>> nsteps  = 5000; 100 ns
>>> dt  = 0.002 ; 2 fs
>>> ; Output control
>>> nstxout = 0  ; suppress .trr output ; output coordinates
>>> every 25 ps
>>> nstvout = 25000 ; velocities to output every 25000 steps
>>> nstenergy   = 1000  ; save energies every 2 ps
>>> nstlog  = 1000  ; update log file every 2 ps
>>> nstxtcout   = 10 ; suppress (tlumic) xtc trajectory
>>> energygrps  = System
>>> continuation= no   ; first dynamics run
>>> constraint_algorithm = lincs; holonomic constraints
>>> constraints = all-bonds ; all bonds (even heavy atom-H bonds)
>>> constrained
>>> lincs_iter  = 1 ; accuracy of LINCS
>>> lincs_order = 4 ; also related to accuracy
>>> ; Neighborsearching
>>> ns_type = grid  ; search neighboring grid cells
>>> nstlist = 5 ; 10 fs
>>> vdwtype = Switch
>>> rvdw-switch = 1.0
>>> rlist   = 1.4   ; short-range neighborlist cutoff (in nm)
>>> rcoulomb= 1.4   ; short-range electrostatic cutoff (in nm)
>>> rvdw= 1.2   ; short-range van der Waals cutoff (in nm)
>>> ewald_rtol  = 1e-5  ; relative strenght of the Ewald-shifted
>>> potential rcoulomb
>>> ; Electrostatics
>>> coulombtype = PME   ; Particle Mesh Ewald for long-range
>>> electrostatics
>>> pme_order   = 4 ; cubic interpolation
>>> fourierspacing  = 0.12  ; grid spacing for FFT
>>> ; Temperature coupling is on
>>> tcoupl  = V-rescale ; modified Berendsen
>>> thermostat
>>> tc_grps = System ; two coupling groups - more
>>> accurate
>>> tau_t   = 0.1 ; time constant, in ps
>>> ref_t   = 318 ; reference temperature, one
>>> for each group, in K
>>> ; Pressure coupling is on
>>> pcoupl  = Parrinello-Rahman ; pressure coupling is on
>>> for 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
>>> ; Periodic boundary conditions
>>> pbc = xyz   ; 3-D PBC
>>> ; Dispersion correction
>>> DispCorr= EnerPres  ; account for cut-off vdW scheme
>>> ; Velocity generation
>>> gen_vel = yes   ; assign velocities from Maxwell distribution
>>> gen_temp= 318   ; temperature for Maxwell distribution
>>> gen_seed= -1; generate a random seed
>>>
>>> Then My log file:
>>>
>>>
>>>  The temperature for test particle insertion is 318.000 K
>>>
>>> Started Test Particle Insertion on node 0 Wed May  9 14:18:18 2012
>>>
>>> Will insert 3 atoms with partial charges
>>>
>>> Will insert 5000 times in each frame of md318.trr
>>> Will use the same neighborlist for 5 insertions in a sphere of radius
>>> 0.05
>>>
>>> = -nan nm^3
>>>= -nan kJ/mol
>>> No MEGA Flopsen this time
>>>
>>>  R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G
>>>
>>>  Computing: Nodes Number G-CyclesSeconds %
>>>

Re: [gmx-users] Test Particle Insertion of Water


The trr file has something wrong. Look at "Coords", it has 0 frames

You may have forgotten to set nstxout to a non-zero value?

Javier

El 09/05/12 16:10, Steven Neumann escribió:

I added one water molecule in my topology to all water molecules:

[ molecules ]
; Compound#mols
Alanine40
SOL   724

Maybe I should add aditional line like:

[ molecules ]
; Compound#mols
Alanine40
SOL   723
SOL  1

What do you think?


On Wed, May 9, 2012 at 3:04 PM, Steven Neumann > wrote:


Checking file md.trr
trn version: GMX_trn_file (single precision)
Reading frame   0 time0.000
# Atoms  2569
Last frame   2000 time 10.000


Item#frames Timestep (ps)
Step  200150
Time  200150
Lambda200150
Coords   0
Velocities200150
Forces   0
Box   200150

Well, it looks ok. Any suggestions?


On Wed, May 9, 2012 at 3:01 PM, Javier Cerezo mailto:j...@um.es>> wrote:

Sorry, I saw now the command line you've posted. Did you check
your trr with gmxcheck?


El 09/05/12 15:49, Steven Neumann escribió:

hello gmx users,


I am sorry for bothering you but I was searching mailing list
and no results. I have a problem with my test particle
insertion as I run the workflow I described previously with
my mdp:

title   = Test Particle Insertion
; Run parameters
integrator  = tpi
nsteps  = 5000; 100 ns
dt  = 0.002 ; 2 fs
; Output control
nstxout = 0  ; suppress .trr output ; output
coordinates every 25 ps
nstvout = 25000 ; velocities to output every 25000 steps
nstenergy   = 1000  ; save energies every 2 ps
nstlog  = 1000  ; update log file every 2 ps
nstxtcout   = 10 ; suppress (tlumic) xtc trajectory
energygrps  = System
continuation= no   ; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = all-bonds ; all bonds (even heavy
atom-H bonds) constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cells
nstlist = 5 ; 10 fs
vdwtype = Switch
rvdw-switch = 1.0
rlist   = 1.4   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.4   ; short-range electrostatic cutoff
(in nm)
rvdw= 1.2   ; short-range van der Waals cutoff
(in nm)
ewald_rtol  = 1e-5  ; relative strenght of the
Ewald-shifted potential rcoulomb
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for
long-range electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.12  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = V-rescale ; modified
Berendsen thermostat
tc_grps = System ; two coupling groups -
more accurate
tau_t   = 0.1 ; time
constant, in ps
ref_t   = 318 ; reference
temperature, one for each group, in K
; Pressure coupling is on
pcoupl  = Parrinello-Rahman ; pressure
coupling is on for 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
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; assign velocities from Maxwell
distribution
gen_temp= 318   ; temperature for Maxwell distribution
gen_seed= -1; generate a random seed

Then My log file:


 The temperature for test particle insertion is 318.000 K

Started Test Particle Insertion on node 0 Wed May  9 14:18:18
2012

Will insert 3 atoms with partial charges

Will insert 5000 times in each frame of md318.trr
Will use the same neighborlist for 5 insertions in a sphere
of radius 0.05

  = -nan nm^3
 = -

Re: [gmx-users] Test Particle Insertion of Water

I added one water molecule in my topology to all water molecules:

[ molecules ]
; Compound#mols
Alanine40
SOL   724

Maybe I should add aditional line like:

[ molecules ]
; Compound#mols
Alanine40
SOL   723
SOL  1

What do you think?


On Wed, May 9, 2012 at 3:04 PM, Steven Neumann wrote:

> Checking file md.trr
> trn version: GMX_trn_file (single precision)
> Reading frame   0 time0.000
> # Atoms  2569
> Last frame   2000 time 10.000
>
>
> Item#frames Timestep (ps)
> Step  200150
> Time  200150
> Lambda200150
> Coords   0
> Velocities200150
> Forces   0
> Box   200150
>
> Well, it looks ok. Any suggestions?
>
>
> On Wed, May 9, 2012 at 3:01 PM, Javier Cerezo  wrote:
>
>>  Sorry, I saw now the command line you've posted. Did you check your trr
>> with gmxcheck?
>>
>>
>> El 09/05/12 15:49, Steven Neumann escribió:
>>
>> hello gmx users,
>>
>>
>> I am sorry for bothering you but I was searching mailing list and no
>> results. I have a problem with my test particle insertion as I run the
>> workflow I described previously with my mdp:
>>
>> title   = Test Particle Insertion
>> ; Run parameters
>> integrator  = tpi
>> nsteps  = 5000; 100 ns
>> dt  = 0.002 ; 2 fs
>> ; Output control
>> nstxout = 0  ; suppress .trr output ; output coordinates
>> every 25 ps
>> nstvout = 25000 ; velocities to output every 25000 steps
>> nstenergy   = 1000  ; save energies every 2 ps
>> nstlog  = 1000  ; update log file every 2 ps
>> nstxtcout   = 10 ; suppress (tlumic) xtc trajectory
>> energygrps  = System
>> continuation= no   ; first dynamics run
>> constraint_algorithm = lincs; holonomic constraints
>> constraints = all-bonds ; all bonds (even heavy atom-H bonds)
>> constrained
>> lincs_iter  = 1 ; accuracy of LINCS
>> lincs_order = 4 ; also related to accuracy
>> ; Neighborsearching
>> ns_type = grid  ; search neighboring grid cells
>> nstlist = 5 ; 10 fs
>> vdwtype = Switch
>> rvdw-switch = 1.0
>> rlist   = 1.4   ; short-range neighborlist cutoff (in nm)
>> rcoulomb= 1.4   ; short-range electrostatic cutoff (in nm)
>> rvdw= 1.2   ; short-range van der Waals cutoff (in nm)
>> ewald_rtol  = 1e-5  ; relative strenght of the Ewald-shifted
>> potential rcoulomb
>> ; Electrostatics
>> coulombtype = PME   ; Particle Mesh Ewald for long-range
>> electrostatics
>> pme_order   = 4 ; cubic interpolation
>> fourierspacing  = 0.12  ; grid spacing for FFT
>> ; Temperature coupling is on
>> tcoupl  = V-rescale ; modified Berendsen
>> thermostat
>> tc_grps = System ; two coupling groups - more accurate
>> tau_t   = 0.1 ; time constant, in ps
>> ref_t   = 318 ; reference temperature, one
>> for each group, in K
>> ; Pressure coupling is on
>> pcoupl  = Parrinello-Rahman ; pressure coupling is on for
>> 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
>> ; Periodic boundary conditions
>> pbc = xyz   ; 3-D PBC
>> ; Dispersion correction
>> DispCorr= EnerPres  ; account for cut-off vdW scheme
>> ; Velocity generation
>> gen_vel = yes   ; assign velocities from Maxwell distribution
>> gen_temp= 318   ; temperature for Maxwell distribution
>> gen_seed= -1; generate a random seed
>>
>> Then My log file:
>>
>>
>>  The temperature for test particle insertion is 318.000 K
>>
>> Started Test Particle Insertion on node 0 Wed May  9 14:18:18 2012
>>
>> Will insert 3 atoms with partial charges
>>
>> Will insert 5000 times in each frame of md318.trr
>> Will use the same neighborlist for 5 insertions in a sphere of radius
>> 0.05
>>
>> = -nan nm^3
>>= -nan kJ/mol
>> No MEGA Flopsen this time
>>
>>  R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G
>>
>>  Computing: Nodes Number G-CyclesSeconds %
>> --
>> -
>>  Rest   4   5.2181.9   100.0
>> ---
>>  Total  4   5.2181.9   100.0
>> ---
>>
>> Parallel run - timing based on wallclock.
>>
>>NODE (s)   Real (s)  (%)
>>T

Re: [gmx-users] Formyl parameters

On 5/9/12 10:02 AM, Shima Arasteh wrote:

OK, I have to build a .rtp file. But I'd like to know if I should make it
corresponding to relation between.itp and .rtp files format?

Start by reading the manual and looking at existing examples.  The formats are 
largely unrelated, but the content of the .itp file will be used to set up the 
.rtp entry.

-Justin

Cheers,
Shima

*From:* Justin A. Lemkul 
*To:* Discussion list for GROMACS users 
*Sent:* Wednesday, May 9, 2012 3:58 PM
*Subject:* Re: [gmx-users] Formyl parameters

On 5/9/12 4:48 AM, Shima Arasteh wrote:
 >
 > Oh my god! :-)
 > The situation seems going complicated! :-(
 > Let me explain what I'm gonna do in detail:
 > I have formyl residue as the N-terminus in my protein (.pdb file) ! As you 
know,
 > the topology database in CHARMM27 doesn't have formyl. So I got its 
parameter as
 > an .itp file through swissparam site. Now I need to include the parameters in
 > the top file. But don't know it well! I just did such as this:
 >
 > 1. seperating the formyl residue from my .pdb file.
 > 2. run pdb2gmx to get top file ( for the .pdb file which doesn't have formyl 
)
 > 3. include the formyl .itp file in my top file
 >
 >
 > Now please let me know if I've done correctly?
 >

No, you haven't. What you've defined now are two separate molecules, when in
fact the formyl group needs to be an added moiety to your protein.

Dealing with this species can be done in one of two ways, both of which require
an .rtp file. Whether or not making a formyl .rtp entry is appropriate is up to
you based on the parameterization you have already done. I would be very
surprised if the presence of the formyl group did not change some aspect (e.g.
charges) of the amino acid to which it is connected. In this case, it is better
in my mind to create an .rtp entry for the complete formylated amino acid,
change residue and/or atom names as necessary in the .pdb file, and run the
entire structure (with the formyl group) through pdb2gmx. The general workflow
for doing all of this (in addition to information in the manual) can be found 
at:

http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

-Justin

-- 

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

-- gmx-users mailing list gmx-users@gromacs.org 
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search
before posting!
Please don't post (un)subscribe requests to the list. Use the www interface or
send it to gmx-users-requ...@gromacs.org .
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

--

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

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

Re: [gmx-users] Test Particle Insertion of Water

Checking file md.trr
trn version: GMX_trn_file (single precision)
Reading frame   0 time0.000
# Atoms  2569
Last frame   2000 time 10.000


Item#frames Timestep (ps)
Step  200150
Time  200150
Lambda200150
Coords   0
Velocities200150
Forces   0
Box   200150

Well, it looks ok. Any suggestions?

On Wed, May 9, 2012 at 3:01 PM, Javier Cerezo  wrote:

>  Sorry, I saw now the command line you've posted. Did you check your trr
> with gmxcheck?
>
>
> El 09/05/12 15:49, Steven Neumann escribió:
>
> hello gmx users,
>
>
> I am sorry for bothering you but I was searching mailing list and no
> results. I have a problem with my test particle insertion as I run the
> workflow I described previously with my mdp:
>
> title   = Test Particle Insertion
> ; Run parameters
> integrator  = tpi
> nsteps  = 5000; 100 ns
> dt  = 0.002 ; 2 fs
> ; Output control
> nstxout = 0  ; suppress .trr output ; output coordinates every
> 25 ps
> nstvout = 25000 ; velocities to output every 25000 steps
> nstenergy   = 1000  ; save energies every 2 ps
> nstlog  = 1000  ; update log file every 2 ps
> nstxtcout   = 10 ; suppress (tlumic) xtc trajectory
> energygrps  = System
> continuation= no   ; first dynamics run
> constraint_algorithm = lincs; holonomic constraints
> constraints = all-bonds ; all bonds (even heavy atom-H bonds)
> constrained
> lincs_iter  = 1 ; accuracy of LINCS
> lincs_order = 4 ; also related to accuracy
> ; Neighborsearching
> ns_type = grid  ; search neighboring grid cells
> nstlist = 5 ; 10 fs
> vdwtype = Switch
> rvdw-switch = 1.0
> rlist   = 1.4   ; short-range neighborlist cutoff (in nm)
> rcoulomb= 1.4   ; short-range electrostatic cutoff (in nm)
> rvdw= 1.2   ; short-range van der Waals cutoff (in nm)
> ewald_rtol  = 1e-5  ; relative strenght of the Ewald-shifted potential
> rcoulomb
> ; Electrostatics
> coulombtype = PME   ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order   = 4 ; cubic interpolation
> fourierspacing  = 0.12  ; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl  = V-rescale ; modified Berendsen thermostat
> tc_grps = System ; two coupling groups - more accurate
> tau_t   = 0.1 ; time constant, in ps
> ref_t   = 318 ; reference temperature, one for
> each group, in K
> ; Pressure coupling is on
> pcoupl  = Parrinello-Rahman ; pressure coupling is on for
> 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
> ; Periodic boundary conditions
> pbc = xyz   ; 3-D PBC
> ; Dispersion correction
> DispCorr= EnerPres  ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel = yes   ; assign velocities from Maxwell distribution
> gen_temp= 318   ; temperature for Maxwell distribution
> gen_seed= -1; generate a random seed
>
> Then My log file:
>
>
>  The temperature for test particle insertion is 318.000 K
>
> Started Test Particle Insertion on node 0 Wed May  9 14:18:18 2012
>
> Will insert 3 atoms with partial charges
>
> Will insert 5000 times in each frame of md318.trr
> Will use the same neighborlist for 5 insertions in a sphere of radius
> 0.05
>
> = -nan nm^3
>= -nan kJ/mol
> No MEGA Flopsen this time
>
>  R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G
>
>  Computing: Nodes Number G-CyclesSeconds %
> --
> -
>  Rest   4   5.2181.9   100.0
> ---
>  Total  4   5.2181.9   100.0
> ---
>
> Parallel run - timing based on wallclock.
>
>NODE (s)   Real (s)  (%)
>Time:  0.485  0.485100.0
>(Mnbf/s)   (MFlops)   (steps/hour)
> Performance:  0.000  0.0000.0
> Finished mdrun on node 0 Wed May  9 14:18:19 2012
>
>
>
> Files are empty. Do you have any clue what is happening?
>
> Thank you for your time,
>
> Steven
>
>
> On Wed, May 9, 2012 at 1:45 PM, Javier Cerezo  wrote:
>
>>  Hi Steven
>>
>> As I remember, TPI is based on the calculation of the potential at every
>> conformation from the already computed simulation (inserting

Re: [gmx-users] Formyl parameters

2012-05-09 Thread Shima Arasteh

OK, I have to build a .rtp file. But I'd like to know if I should make it 
corresponding to relation between.itp and .rtp files format?

Cheers,
Shima

 From: Justin A. Lemkul 
To: Discussion list for GROMACS users  
Sent: Wednesday, May 9, 2012 3:58 PM
Subject: Re: [gmx-users] Formyl parameters

On 5/9/12 4:48 AM, Shima Arasteh wrote:
> 
> Oh my god! :-)
> The situation seems going complicated! :-(
> Let me explain what I'm gonna do in detail:
> I have formyl residue as the N-terminus in my protein (.pdb file) ! As you 
> know,
> the topology database in CHARMM27 doesn't have formyl. So I got its parameter 
> as
> an .itp file through swissparam site. Now I need to include the parameters in
> the top file. But don't know it well! I just did such as this:
> 
> 1. seperating the formyl residue from my .pdb file.
> 2. run pdb2gmx to get top file ( for the .pdb file which doesn't have formyl )
> 3. include the formyl .itp file in my top file
> 
> 
> Now please let me know if I've done correctly?
> 

No, you haven't.  What you've defined now are two separate molecules, when in 
fact the formyl group needs to be an added moiety to your protein.

Dealing with this species can be done in one of two ways, both of which require 
an .rtp file.  Whether or not making a formyl .rtp entry is appropriate is up 
to you based on the parameterization you have already done.  I would be very 
surprised if the presence of the formyl group did not change some aspect (e.g. 
charges) of the amino acid to which it is connected.  In this case, it is 
better in my mind to create an .rtp entry for the complete formylated amino 
acid, change residue and/or atom names as necessary in the .pdb file, and run 
the entire structure (with the formyl group) through pdb2gmx.  The general 
workflow for doing all of this (in addition to information in the manual) can 
be found at:

http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

-Justin

-- 

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

-- gmx-users mailing list    gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface or 
send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Test Particle Insertion of Water

Sorry, I saw now the command line you've posted. Did you check your trr 
with gmxcheck?


El 09/05/12 15:49, Steven Neumann escribió:

hello gmx users,

I am sorry for bothering you but I was searching mailing list and no 
results. I have a problem with my test particle insertion as I run the 
workflow I described previously with my mdp:


title   = Test Particle Insertion
; Run parameters
integrator  = tpi
nsteps  = 5000; 100 ns
dt  = 0.002 ; 2 fs
; Output control
nstxout = 0  ; suppress .trr output ; output coordinates 
every 25 ps

nstvout = 25000 ; velocities to output every 25000 steps
nstenergy   = 1000  ; save energies every 2 ps
nstlog  = 1000  ; update log file every 2 ps
nstxtcout   = 10 ; suppress (tlumic) xtc trajectory
energygrps  = System
continuation= no   ; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds) 
constrained

lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cells
nstlist = 5 ; 10 fs
vdwtype = Switch
rvdw-switch = 1.0
rlist   = 1.4   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.4   ; short-range electrostatic cutoff (in nm)
rvdw= 1.2   ; short-range van der Waals cutoff (in nm)
ewald_rtol  = 1e-5  ; relative strenght of the Ewald-shifted 
potential rcoulomb

; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range 
electrostatics

pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.12  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = V-rescale ; modified Berendsen 
thermostat

tc_grps = System ; two coupling groups - more accurate
tau_t   = 0.1 ; time constant, in ps
ref_t   = 318 ; reference temperature, one 
for each group, in K

; Pressure coupling is on
pcoupl  = Parrinello-Rahman ; pressure coupling is on 
for 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

; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; assign velocities from Maxwell distribution
gen_temp= 318   ; temperature for Maxwell distribution
gen_seed= -1; generate a random seed

Then My log file:


 The temperature for test particle insertion is 318.000 K

Started Test Particle Insertion on node 0 Wed May  9 14:18:18 2012

Will insert 3 atoms with partial charges

Will insert 5000 times in each frame of md318.trr
Will use the same neighborlist for 5 insertions in a sphere of radius 
0.05


  = -nan nm^3
 = -nan kJ/mol
No MEGA Flopsen this time

 R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G

 Computing: Nodes Number G-CyclesSeconds %
--
-
 Rest   4   5.2181.9   100.0
---
 Total  4   5.2181.9   100.0
---

Parallel run - timing based on wallclock.

   NODE (s)   Real (s)  (%)
   Time:  0.485  0.485100.0
   (Mnbf/s)   (MFlops)   (steps/hour)
Performance:  0.000  0.0000.0
Finished mdrun on node 0 Wed May  9 14:18:19 2012



Files are empty. Do you have any clue what is happening?

Thank you for your time,

Steven


On Wed, May 9, 2012 at 1:45 PM, Javier Cerezo > wrote:


Hi Steven

As I remember, TPI is based on the calculation of the potential at
every conformation from the already computed simulation (inserting
the particle in every snapshot), so velocities are not used.

Anyway, use both and see if there are any differences.

Javier

El 09/05/12 11:27, Steven Neumann escribió:

Dear Gmx Users,

I am running TPI of the water in the system containing free amino
acids. Steps:

1. I run the NPT simulation of 100 ns to equilibrate the system.
2. I added 1 extra water molecule to the final pdb file
(converted from gro) and to topology
3. I creaded tpi.tpr using grompp using new pdb file with extra
water molecule
4. mdrun --s tpi298.tpr -rerun md298.trr -deffnm tpi298 -t

Re: [gmx-users] Test Particle Insertion of Water

grompp -f tpi.mdp -c tpi.pdb -p topol.top -o tpi.tpr

where tpi.pdb is a file with extra water molecule as well as topol.top.
Then:

mdrun –s tpi.tpr -rerun md.trr -deffnm tpi -tpi tpi.xvg -tpid tpid.xvg



On Wed, May 9, 2012 at 2:56 PM, Javier Cerezo  wrote:

> What's your command line?
>
> El 09/05/12 15:49, Steven Neumann escribió:
>
>  title   = Test Particle Insertion
>> ; Run parameters
>> integrator  = tpi
>> nsteps  = 5000; 100 ns
>> dt  = 0.002 ; 2 fs
>> ; Output control
>> nstxout = 0  ; suppress .trr output ; output coordinates
>> every 25 ps
>> nstvout = 25000 ; velocities to output every 25000 steps
>> nstenergy   = 1000  ; save energies every 2 ps
>> nstlog  = 1000  ; update log file every 2 ps
>> nstxtcout   = 10 ; suppress (tlumic) xtc trajectory
>> energygrps  = System
>> continuation= no   ; first dynamics run
>> constraint_algorithm = lincs; holonomic constraints
>> constraints = all-bonds ; all bonds (even heavy atom-H bonds)
>> constrained
>> lincs_iter  = 1 ; accuracy of LINCS
>> lincs_order = 4 ; also related to accuracy
>> ; Neighborsearching
>> ns_type = grid  ; search neighboring grid cells
>> nstlist = 5 ; 10 fs
>> vdwtype = Switch
>> rvdw-switch = 1.0
>> rlist   = 1.4   ; short-range neighborlist cutoff (in nm)
>> rcoulomb= 1.4   ; short-range electrostatic cutoff (in nm)
>> rvdw= 1.2   ; short-range van der Waals cutoff (in nm)
>> ewald_rtol  = 1e-5  ; relative strenght of the Ewald-shifted
>> potential rcoulomb
>> ; Electrostatics
>> coulombtype = PME   ; Particle Mesh Ewald for long-range
>> electrostatics
>> pme_order   = 4 ; cubic interpolation
>> fourierspacing  = 0.12  ; grid spacing for FFT
>> ; Temperature coupling is on
>> tcoupl  = V-rescale ; modified Berendsen
>> thermostat
>> tc_grps = System ; two coupling groups - more accurate
>> tau_t   = 0.1 ; time constant, in ps
>> ref_t   = 318 ; reference temperature, one
>> for each group, in K
>> ; Pressure coupling is on
>> pcoupl  = Parrinello-Rahman ; pressure coupling is on for
>> 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
>> ; Periodic boundary conditions
>> pbc = xyz   ; 3-D PBC
>> ; Dispersion correction
>> DispCorr= EnerPres  ; account for cut-off vdW scheme
>> ; Velocity generation
>> gen_vel = yes   ; assign velocities from Maxwell distribution
>> gen_temp= 318   ; temperature for Maxwell distribution
>> gen_seed= -1; generate a random seed
>>
>
> --
> Javier CEREZO BASTIDA
> PhD Student
> Physical Chemistry
> Universidad de Murcia
> Murcia (Spain)
> Tel: (+34)868887434
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Test Particle Insertion of Water


What's your command line?

El 09/05/12 15:49, Steven Neumann escribió:

title   = Test Particle Insertion
; Run parameters
integrator  = tpi
nsteps  = 5000; 100 ns
dt  = 0.002 ; 2 fs
; Output control
nstxout = 0  ; suppress .trr output ; output coordinates 
every 25 ps

nstvout = 25000 ; velocities to output every 25000 steps
nstenergy   = 1000  ; save energies every 2 ps
nstlog  = 1000  ; update log file every 2 ps
nstxtcout   = 10 ; suppress (tlumic) xtc trajectory
energygrps  = System
continuation= no   ; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds) 
constrained

lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cells
nstlist = 5 ; 10 fs
vdwtype = Switch
rvdw-switch = 1.0
rlist   = 1.4   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.4   ; short-range electrostatic cutoff (in nm)
rvdw= 1.2   ; short-range van der Waals cutoff (in nm)
ewald_rtol  = 1e-5  ; relative strenght of the Ewald-shifted 
potential rcoulomb

; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range 
electrostatics

pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.12  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = V-rescale ; modified Berendsen 
thermostat

tc_grps = System ; two coupling groups - more accurate
tau_t   = 0.1 ; time constant, in ps
ref_t   = 318 ; reference temperature, one 
for each group, in K

; Pressure coupling is on
pcoupl  = Parrinello-Rahman ; pressure coupling is on 
for 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

; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; assign velocities from Maxwell distribution
gen_temp= 318   ; temperature for Maxwell distribution
gen_seed= -1; generate a random seed


--
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tel: (+34)868887434
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

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

Re: [gmx-users] Test Particle Insertion of Water

hello gmx users,

I am sorry for bothering you but I was searching mailing list and no
results. I have a problem with my test particle insertion as I run the
workflow I described previously with my mdp:

title   = Test Particle Insertion
; Run parameters
integrator  = tpi
nsteps  = 5000; 100 ns
dt  = 0.002 ; 2 fs
; Output control
nstxout = 0  ; suppress .trr output ; output coordinates every
25 ps
nstvout = 25000 ; velocities to output every 25000 steps
nstenergy   = 1000  ; save energies every 2 ps
nstlog  = 1000  ; update log file every 2 ps
nstxtcout   = 10 ; suppress (tlumic) xtc trajectory
energygrps  = System
continuation= no   ; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cells
nstlist = 5 ; 10 fs
vdwtype = Switch
rvdw-switch = 1.0
rlist   = 1.4   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.4   ; short-range electrostatic cutoff (in nm)
rvdw= 1.2   ; short-range van der Waals cutoff (in nm)
ewald_rtol  = 1e-5  ; relative strenght of the Ewald-shifted potential
rcoulomb
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.12  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = V-rescale ; modified Berendsen thermostat
tc_grps = System ; two coupling groups - more accurate
tau_t   = 0.1 ; time constant, in ps
ref_t   = 318 ; reference temperature, one for
each group, in K
; Pressure coupling is on
pcoupl  = Parrinello-Rahman ; pressure coupling is on for
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
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; assign velocities from Maxwell distribution
gen_temp= 318   ; temperature for Maxwell distribution
gen_seed= -1; generate a random seed

Then My log file:


 The temperature for test particle insertion is 318.000 K

Started Test Particle Insertion on node 0 Wed May  9 14:18:18 2012

Will insert 3 atoms with partial charges

Will insert 5000 times in each frame of md318.trr
Will use the same neighborlist for 5 insertions in a sphere of radius
0.05

= -nan nm^3
   = -nan kJ/mol
No MEGA Flopsen this time

 R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G

 Computing: Nodes Number G-CyclesSeconds %
--
-
 Rest   4   5.2181.9   100.0
---
 Total  4   5.2181.9   100.0
---

Parallel run - timing based on wallclock.

   NODE (s)   Real (s)  (%)
   Time:  0.485  0.485100.0
   (Mnbf/s)   (MFlops)   (steps/hour)
Performance:  0.000  0.0000.0
Finished mdrun on node 0 Wed May  9 14:18:19 2012



Files are empty. Do you have any clue what is happening?

Thank you for your time,

Steven


On Wed, May 9, 2012 at 1:45 PM, Javier Cerezo  wrote:

>  Hi Steven
>
> As I remember, TPI is based on the calculation of the potential at every
> conformation from the already computed simulation (inserting the particle
> in every snapshot), so velocities are not used.
>
> Anyway, use both and see if there are any differences.
>
> Javier
>
> El 09/05/12 11:27, Steven Neumann escribió:
>
> Dear Gmx Users,
>
> I am running TPI of the water in the system containing free amino acids.
> Steps:
>
> 1. I run the NPT simulation of 100 ns to equilibrate the system.
> 2. I added 1 extra water molecule to the final pdb file (converted from
> gro) and to topology
> 3. I creaded tpi.tpr using grompp using new pdb file with extra water
> molecule
> 4. mdrun –s tpi298.tpr -rerun md298.trr -deffnm tpi298 -tpi tpi298.xvg
> -tpid tpid298.xvg
>
> My question: Is it better generate new velocities in my mdp file
> (continuation = yes, gen_vel = no, tpi integrator) for a pdb file or use
> velocities from pre

Re: [gmx-users] pdb2gmx angles and dihedrals

2012-05-09 Thread Elton Carvalho

On Tue, May 8, 2012 at 2:04 AM, Mark Abraham  wrote:
>
>
> Yeah, that .rtp comment looks totally wrong. After looking at the code I
> think:
>
>    * Column 5: 1 means keep all generated dihedrals,
>    *   0 means permit generated dihedrals to have their parameters
>    *  superseded by ones on the same central bond that have
>    *  fewer hydrogen atoms.
>
> That's totally different from what the .itp suggests, and does explain your
> observations.
>
> There seems to be no automatic way to treat the issue that you'd like
> addressed. Feel free to make a feature request on redmine.gromacs.org, but
> it likely won't be addressed until GROMACS 5 (at least).
>

Thanks, Mark. I think, though, that this case is too specific for a
feature-request. I was just hoping to have an automated tool to do
this boring part.

I guess I'll just postprocess the topology with a script after it's
generated by pdb2gmx.

Good to know that this sparkled some reviewing of the code and the manual =)

>
> There have been quite a few manual updates already. For example,
> http://jenkins.gromacs.org/job/Manual_Gerrit_4_5/15/ has a link to a current
> PDF manual ("save as" on the PDF link is sometimes necessary). Feedback is
> welcome, but feedback relative to the updated manual is more welcome. :-)
>

Great. I looked at yesterday's build, right before the reversion and
followed some of the discussion on Gerrit.

I'll submit my suggestions to the redmine site to avoid cluttering the list.

Thanks for the help!
-- 
Elton Carvalho
Tel.: +55 11 3091-6985/6922
Dept Física dos Materiais e Mecânica
Instituto de Física
Universidade de São Paulo
P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Bonds between planar group of atoms

Dear Gmx Users,

My surface is made of different atoms (Fe, Na, H). I would like to create
bonds between them so the surface will be stable. Is there a command in
gromacs to create [ bonds ] and to add to your topology?
I tried to use specbond.dat but none bonds were created. It could be
manually quite time consuming.

Thank you

Steven
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Test Particle Insertion of Water

thank you Javier, I will try both in this case.

On Wed, May 9, 2012 at 1:45 PM, Javier Cerezo  wrote:

>  Hi Steven
>
> As I remember, TPI is based on the calculation of the potential at every
> conformation from the already computed simulation (inserting the particle
> in every snapshot), so velocities are not used.
>
> Anyway, use both and see if there are any differences.
>
> Javier
>
> El 09/05/12 11:27, Steven Neumann escribió:
>
> Dear Gmx Users,
>
> I am running TPI of the water in the system containing free amino acids.
> Steps:
>
> 1. I run the NPT simulation of 100 ns to equilibrate the system.
> 2. I added 1 extra water molecule to the final pdb file (converted from
> gro) and to topology
> 3. I creaded tpi.tpr using grompp using new pdb file with extra water
> molecule
> 4. mdrun –s tpi298.tpr -rerun md298.trr -deffnm tpi298 -tpi tpi298.xvg
> -tpid tpid298.xvg
>
> My question: Is it better generate new velocities in my mdp file
> (continuation = yes, gen_vel = no, tpi integrator) for a pdb file or use
> velocities from previous simulations (gro file)?
> If the second option is more appropriate what velocity shall I adjust to
> the extra water molecule?
>
> I will appreciate your reply.
>
> Steven
>
>
>
> --
> Javier CEREZO BASTIDA
> PhD Student
> Physical Chemistry
> Universidad de Murcia
> Murcia (Spain)
> Tel: (+34)868887434
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Test Particle Insertion of Water


Hi Steven

As I remember, TPI is based on the calculation of the potential at every 
conformation from the already computed simulation (inserting the 
particle in every snapshot), so velocities are not used.


Anyway, use both and see if there are any differences.

Javier

El 09/05/12 11:27, Steven Neumann escribió:

Dear Gmx Users,

I am running TPI of the water in the system containing free amino 
acids. Steps:


1. I run the NPT simulation of 100 ns to equilibrate the system.
2. I added 1 extra water molecule to the final pdb file (converted 
from gro) and to topology
3. I creaded tpi.tpr using grompp using new pdb file with extra water 
molecule
4. mdrun --s tpi298.tpr -rerun md298.trr -deffnm tpi298 -tpi 
tpi298.xvg -tpid tpid298.xvg


My question: Is it better generate new velocities in my mdp file 
(continuation = yes, gen_vel = no, tpi integrator) for a pdb file or 
use velocities from previous simulations (gro file)?
If the second option is more appropriate what velocity shall I adjust 
to the extra water molecule?


I will appreciate your reply.

Steven




--
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tel: (+34)868887434
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Go model -error in generating topology




On 5/9/12 8:37 AM, mohan maruthi sena wrote:

Hi all,
   I try to build go model(which uses only c-alpha atoms), my pdb
contains only c-alpha atoms extracted from the original pdb file ,when i use
pdb2gmx command on c-alpha containing pdb file it gives the following error.

 Atom N is used in an interaction of type atom in the topology
   database, but an atom of that name was not found in residue
 number 1.
Please suggest me a way ,



pdb2gmx is not suited for building such a topology.

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

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

[gmx-users] Go model -error in generating topology

2012-05-09 Thread mohan maruthi sena

Hi all,
  I try to build go model(which uses only c-alpha atoms), my pdb
contains only c-alpha atoms extracted from the original pdb file ,when i
use pdb2gmx command on c-alpha containing pdb file it gives the following
error.

Atom N is used in an interaction of type atom in the topology
  database, but an atom of that name was not found in residue
number 1.
Please suggest me a way ,

Thanking you in advance,
Mohan
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Itp file problem -- Atom type not found




On 5/9/12 3:13 AM, Sarath Kumar Baskaran wrote:

Hi Justin,

I had used only  Gromos 43 a1 from initially for proteins, but i saw the -ff gmx
in the Drug enzyme tutorial, so i tried using this optiion for protein ligand
comp[ex simultaitons, also the simulation was able to be performed with -ff gmx
for some ligands without the atom type not found error. for all the ligands i
used the itp (topology) file from PRODRG only


Depending on which version of PRODRG you used, this approach may or may not have 
been appropriate.  I'm assuming the tutorial you followed was John Kerrigan's, 
which is several years old and relies on an older version of PRODRG.  In any 
case, unmodified PRODRG parameters are insufficiently accurate for simulations, 
in every case that I have seen.  There are better tools available, and greater 
detail in parameterization is expected.  Interpret your results with care, and 
don't be shocked if reviewers of your papers do not believe the PRODRG results.



I came accross the problem that u stated with PRODRG in the archives...
Now for this protein ligand complex i am unable to used Gromos43a1, it says
number of atoms mismatch
but that problem of mismatch is due to the itp file included in the .top file
For complexes i do add the .itp file in the .top file everytime during 
simulation...
If in case the only way to solve this problem is to make manual improvements in
the itp file
Can u please help me how to do the adjustmentsI am sorry i dont know how to
create a manual itp topology file...



Mismatch between coordinate and topology files is simply due to incorrect 
counting of molecules or failure to maintain a match between the two.  The 
solution is always the same - take greater care in bookkeeping throughout your 
workflow.  Any time the coordinate file is changed, so too must the topology. 
Some tools (genbox, genion) do this for you.  Anything else is up to you to 
verify and apply.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

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

Re: [gmx-users] Formyl parameters




On 5/9/12 4:48 AM, Shima Arasteh wrote:


Oh my god! :-)
The situation seems going complicated! :-(
Let me explain what I'm gonna do in detail:
I have formyl residue as the N-terminus in my protein (.pdb file) ! As you know,
the topology database in CHARMM27 doesn't have formyl. So I got its parameter as
an .itp file through swissparam site. Now I need to include the parameters in
the top file. But don't know it well! I just did such as this:

1. seperating the formyl residue from my .pdb file.
2. run pdb2gmx to get top file ( for the .pdb file which doesn't have formyl )
3. include the formyl .itp file in my top file


Now please let me know if I've done correctly?



No, you haven't.  What you've defined now are two separate molecules, when in 
fact the formyl group needs to be an added moiety to your protein.


Dealing with this species can be done in one of two ways, both of which require 
an .rtp file.  Whether or not making a formyl .rtp entry is appropriate is up to 
you based on the parameterization you have already done.  I would be very 
surprised if the presence of the formyl group did not change some aspect (e.g. 
charges) of the amino acid to which it is connected.  In this case, it is better 
in my mind to create an .rtp entry for the complete formylated amino acid, 
change residue and/or atom names as necessary in the .pdb file, and run the 
entire structure (with the formyl group) through pdb2gmx.  The general workflow 
for doing all of this (in addition to information in the manual) can be found at:


http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

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

[gmx-users] Test Particle Insertion of Water