Re: [gmx-users] Need protein-ligand free energy calculation tutorial

[Sergey Filkin]

Actually,
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/
there are two different manuals - one about free energy calculation and
other about protein ligand complexes.

This page is also can be helpfull
http://www.alchemistry.org/wiki/Category:Free_Energy_How-to%27s


2013/9/19 Naga Sundar 

> Dear Gromacs users
>
>-- Iam trying to perform free energy calculation for
> protein-ligand complex.
>--Can any one plz suggess an appropriate tutorial to be
> follow to perform this analysis
> --
> Thanks & Regards
> N.NagaSundaram
> --
> gmx-users mailing listgmx-users@gromacs.org
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-- 
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Researcher
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[gmx-users] Re: Need protein-ligand free energy calculation tutorial

[hsp85]

Actually,
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/
there are two different manuals - one about free energy calculation and
other about protein ligand complexes.
 
This page is also can be helpfull
http://www.alchemistry.org/wiki/Category:Free_Energy_How-to%27s

Sergey Filkin

--
View this message in context: 
http://gromacs.5086.x6.nabble.com/Need-protein-ligand-free-energy-calculation-tutorial-tp5011299p5011302.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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Re: [gmx-users] performance issue with the parallel implementation of gromacs

[Carsten Kutzner]

Hi,

make a scaling test and run on a single node only at first. So you can
estimate what performance you can at most expect when going to more nodes.

On a single node, you can also run with Gromacs' thread-MPI, thus 
eliminating the possibility that something with your MPI is wrong.

There are lots of reasons why your parallel performance could be bad.
Can you check that actually the Infiniband interconnect is used and
not the Ethernet? It could also be that a single process is still
running on any of your cores and eating up CPU time. Or maybe the
pinning of threads to cores is not correct (what does md.log say
about that?).

Just a few ideas.

Good luck!

Carsten


On Sep 19, 2013, at 8:07 AM, ashutosh srivastava  wrote:

> Hi
> 
> I have been trying to run simulation on a cluster consisting of 24 nodes
> Intel(R) Xeon(R) CPU X5670 @ 2.93GHz. Each node has 12 processors and they
> are connected via 1Gbit Ethernet and Infiniband interconnect. The batch
> system is TORQUE. However due to some issues with the parallel queue I have
> been trying to run the simulations directly on the cluster using mpdboot
> and mpirun.
> Following is the mdp.out file that I am using for simulation
> ; VARIOUS PREPROCESSING OPTIONS
> ; Preprocessor information: use cpp syntax.
> ; e.g.: -I/home/joe/doe -I/home/mary/roe
> include  =
> ; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)
> define   = -DPOSRES
> 
> ; RUN CONTROL PARAMETERS
> integrator   = md
> ; Start time and timestep in ps
> tinit= 0
> dt   = 0.002
> nsteps   = 25
> ; For exact run continuation or redoing part of a run
> init-step= 0
> ; Part index is updated automatically on checkpointing (keeps files
> separate)
> simulation-part  = 1
> ; mode for center of mass motion removal
> comm-mode= Linear
> ; number of steps for center of mass motion removal
> nstcomm  = 100
> ; group(s) for center of mass motion removal
> comm-grps=
> 
> ; LANGEVIN DYNAMICS OPTIONS
> ; Friction coefficient (amu/ps) and random seed
> bd-fric  = 0
> ld-seed  = 1993
> 
> ; ENERGY MINIMIZATION OPTIONS
> ; Force tolerance and initial step-size
> emtol= 10
> emstep   = 0.01
> ; Max number of iterations in relax-shells
> niter= 20
> ; Step size (ps^2) for minimization of flexible constraints
> fcstep   = 0
> ; Frequency of steepest descents steps when doing CG
> nstcgsteep   = 1000
> nbfgscorr= 10
> 
> ; TEST PARTICLE INSERTION OPTIONS
> rtpi = 0.05
> 
> ; OUTPUT CONTROL OPTIONS
> ; Output frequency for coords (x), velocities (v) and forces (f)
> nstxout  = 100
> nstvout  = 100
> nstfout  = 0
> ; Output frequency for energies to log file and energy file
> nstlog   = 100
> nstcalcenergy= 100
> nstenergy= 100
> ; Output frequency and precision for .xtc file
> nstxtcout= 0
> xtc-precision= 1000
> ; This selects the subset of atoms for the .xtc file. You can
> ; select multiple groups. By default all atoms will be written.
> xtc-grps =
> ; Selection of energy groups
> energygrps   =
> 
> ; NEIGHBORSEARCHING PARAMETERS
> ; cut-off scheme (group: using charge groups, Verlet: particle based
> cut-offs)
> cutoff-scheme= Group
> ; nblist update frequency
> nstlist  = 5
> ; ns algorithm (simple or grid)
> ns_type  = grid
> ; Periodic boundary conditions: xyz, no, xy
> pbc  = xyz
> periodic-molecules   = no
> ; Allowed energy drift due to the Verlet buffer in kJ/mol/ps per atom,
> ; a value of -1 means: use rlist
> verlet-buffer-drift  = 0.005
> ; nblist cut-off
> rlist= 1.0
> ; long-range cut-off for switched potentials
> rlistlong= -1
> nstcalclr= -1
> 
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> ; Method for doing electrostatics
> coulombtype  = PME
> coulomb-modifier = Potential-shift-Verlet
> rcoulomb-switch  = 0
> rcoulomb = 1.0
> ; Relative dielectric constant for the medium and the reaction field
> epsilon-r= 1
> epsilon-rf   = 0
> ; Method for doing Van der Waals
> vdw-type = Cut-off
> vdw-modifier = Potential-shift-Verlet
> ; cut-off lengths
> rvdw-switch  = 0
> rvdw = 1.0
> ; Apply long range dispersion corrections for Energy and Pressure
> DispCorr = EnerPres
> ; Extension of the potential lookup tables beyond the cut-off
> table-extension  = 1
> ; Separate tables between energy group pairs
> energygrp-table  =
> ; Sp

[gmx-users] control atom in .hdb file

[xiao]

Dear all,
 
I am developing the force field paramters of an organic molecule. I have a 
trouble when i wrote the hydrogen atom database (.hdb) file. I do not know how 
to write to control atom. The manual said that:

Three or four control atoms (i,j,k,l), where the first always is the atom to 
which the H atoms are connected. The other two or three depend on the code 
selected.  I can know the meaning of the first control atom, but i am confused 
by "The other two or three depend on the code selected". I think the other two 
control atoms are the heavy atoms that are the neighbor of the heavy atom that 
is needed to add hydrogen. But how to define the control atoms for the -CH3 
group, because there is only one heavy atom that is connected to the -CH3 group?

Any suggestion is appreciated.

Best wishes

Fugui
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Re: [gmx-users] modify nsteps in an existing tpr file

[Mark Abraham]

Indeed - your question was fair, and no undue criticism pertained! :-)
If you are trying to reproduce something, you must expect .tpr
differences between 4.0.x and 4.6.y. I illustrated the change that has
taken place in how VDW parameters are used internally in 4.6, and how
that is distinct from the (presumably) unchanged description of those
parameters. How and where to document this kind of thing so that
people who need it can find it and those who don't need it don't drown
in paper is an impossible problem!

Cheers,

Mark

On Wed, Sep 18, 2013 at 8:34 PM, Guanglei Cui
 wrote:
> It is only a simple question, not a criticism of any kind. I'm sure there
> may be perfect reasons to choose one implementation over another. To
> someone who is not familiar with the history of gmx development, it is
> something to be aware of. That's all.
>
>
> On Wed, Sep 18, 2013 at 4:56 PM, Mark Abraham wrote:
>
>> Implementation and description of a model physics are two different
>> things. You could compute KE of a particle with 0.5 * m * v^2, but if
>> the mass is used nowhere else, why wouldn't you pre-multiply the mass
>> by 0.5?
>>
>> Mark
>>
>> On Wed, Sep 18, 2013 at 4:31 PM, Guanglei Cui
>>  wrote:
>> > hmm, does that mean the gmx force field file format or specifications are
>> > not backward compatible?
>> >
>> >
>> > On Wed, Sep 18, 2013 at 4:08 PM, Mark Abraham > >wrote:
>> >
>> >> There are technical differences between versions about how the VDW
>> >> parameters are computed. You should not expect .tpr equivalence
>> >> between minor version changes such as 4.0 and 4.6. You need to compile
>> >> a 4.0.x grompp to see if your setup is equivalent, but having done so
>> >> you should be able to use the same inputs to 4.6 grompp and get a
>> >> correct simulation with 4.6 mdrun.
>> >>
>> >> Mark
>> >>
>> >> On Wed, Sep 18, 2013 at 1:55 PM, Guanglei Cui
>> >>  wrote:
>> >> > Thanks. gmxcheck is quite helpful. Here is part of the output. It
>> turns
>> >> out
>> >> > the difference is mainly in the force field parameters, which
>> indicates
>> >> the
>> >> > top file provided may not be the one used to produce the tpr file.
>> >> Perhaps
>> >> > it is best to contact the authors, unless the difference is due to
>> >> certain
>> >> > changes between gmx 4.0.x and gmx 4.6.3.
>> >> >
>> >> > inputrec->nsteps (5000 - 5000)
>> >> > inputrec->nstcalclr (5 - 0)
>> >> > inputrec->nstdhdl (1 - 50)
>> >> > inputrec->fepvals->init_fep_state ( 0.0e+00 -
>> -1.0e+00)
>> >> > inputrec->fepvals->lambda_neighbors[1] (0 - 1)
>> >> > inputrec->fepvals->sc_power (0 - 1)
>> >> > inputrec->dihre_fc (1.00e+03 - 0.00e+00)
>> >> > inputrec->grpopts.ngtc (4 - 1)
>> >> > inputrec->grpopts.ngener (4 - 1)
>> >> > inputrec->grpopts.nrdf[ 0] (8.610900e+04 - 2.136210e+05)
>> >> > idef->iparam[12]1: c6= 4.23112651e-03, c12= 4.76949208e-06
>> >> > idef->iparam[12]2: c6= 4.68938737e-08, c12= 1.15147106e-12
>> >> > idef->iparam[54]1: c6= 4.58155479e-03, c12= 4.48611081e-06
>> >> > idef->iparam[54]2: c6= 4.46544206e-08, c12= 8.37594751e-13
>> >> > idef->iparam[82]1: c6= 3.75142763e-03, c12= 4.22875655e-06
>> >> > idef->iparam[82]2: c6= 4.15773336e-08, c12= 1.02092445e-12
>> >> > idef->iparam[96]1: c6= 3.8381e-03, c12= 2.83264171e-06
>> >> > idef->iparam[96]2: c6= 2.83739432e-08, c12= 3.04270091e-13
>> >> > idef->iparam[124]1: c6= 4.26879199e-03, c12= 3.50070763e-06
>> >> > idef->iparam[124]2: c6= 3.50897622e-08, c12= 4.64908439e-13
>> >> > idef->iparam[152]1: c6= 3.59375845e-03, c12= 2.76020933e-06
>> >> > idef->iparam[152]2: c6= 2.76677472e-08, c12= 3.21553060e-13
>> >> > idef->iparam[166]1: c6= 7.79988989e-03, c12= 1.19875567e-05
>> >> > idef->iparam[166]2: c6= 1.12529349e-07, c12= 4.90395051e-12
>> >> > idef->iparam[168]1: c6= 4.23112651e-03, c12= 4.76949208e-06
>> >> > idef->iparam[168]2: c6= 4.68938737e-08, c12= 1.15147106e-12
>> >> > idef->iparam[171]1: c6= 4.58155479e-03, c12= 4.48611081e-06
>> >> > idef->iparam[171]2: c6= 4.46544206e-08, c12= 8.37594751e-13
>> >> > idef->iparam[173]1: c6= 3.75142763e-03, c12= 4.22875655e-06
>> >> > idef->iparam[173]2: c6= 4.15773336e-08, c12= 1.02092445e-12
>> >> > idef->iparam[174]1: c6= 3.8381e-03, c12= 2.83264171e-06
>> >> > idef->iparam[174]2: c6= 2.83739432e-08, c12= 3.04270091e-13
>> >> > idef->iparam[176]1: c6= 4.26879199e-03, c12= 3.50070763e-06
>> >> > idef->iparam[176]2: c6= 3.50897622e-08, c12= 4.64908439e-13
>> >> > idef->iparam[178]1: c6= 3.59375845e-03, c12= 2.76020933e-06
>> >> > idef->iparam[178]2: c6= 2.76677472e-08, c12= 3.21553060e-13
>> >> > idef->iparam[179]1: c6= 7.79988989e-03, c12= 1.19875567e-05
>> >> > idef->iparam[179]2: c6= 1.12529349e-07, c12= 4.90395051e-12
>> >> > idef->iparam[180]1: c6= 6.22385694e-03, c12= 5.03394313e-06
>> >> > idef->iparam[180]2: c6= 2.05496373e-24, c12= 0.e+00
>> >> > idef->iparam[181]1: c6= 3.93928867e-03, c12= 3.50622463e-06
>> >> > idef->iparam[181]2: c6= 3.50750256e-08, c12= 5.46337281e-13
>> >> > idef->iparam

Re: [gmx-users] Selecting certain types of atoms from trajectory file with C++ code

[Justin Lemkul]

On 9/19/13 12:33 AM, Zhikun wrote:

Dear users,

Recently I have been trying to use "xdrfile" libray to read trajectory
".trr" file in my own C++ code. Now I can just read the coordinates of  all
atoms at each time frame. But I don't know how to select certain types of
atoms from the trajectory file. Although the graomcs tool "make_ndx" can do
this, but i need to do it with C++ codes for the purpose of further
analysis. Does someone have any experience about this? Your reply would be
greatly appreciated.



Atom names, types, etc are not stored in trajectories at all.  They are in 
topologies (.top/.tpr) so you need to get the information from those file types.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] control atom in .hdb file

[Justin Lemkul]

On 9/19/13 5:40 AM, xiao wrote:

Dear all,

I am developing the force field paramters of an organic molecule. I have a 
trouble when i wrote the hydrogen atom database (.hdb) file. I do not know how 
to write to control atom. The manual said that:

Three or four control atoms (i,j,k,l), where the first always is the atom to which the H 
atoms are connected. The other two or three depend on the code selected.  I can know the 
meaning of the first control atom, but i am confused by "The other two or three 
depend on the code selected". I think the other two control atoms are the heavy 
atoms that are the neighbor of the heavy atom that is needed to add hydrogen. But how to 
define the control atoms for the -CH3 group, because there is only one heavy atom that is 
connected to the -CH3 group?



The control atoms are chosen based on the geometry of the group.  Exact 
specifications are given in manual section 5.6.4.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] Re: Need protein-ligand free energy calculation tutorial

[Michael Shirts]

There are some starter files here:

http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_free_energy_calculations%3a_Michael_Shirts%2c_Session_2A

Which can be used in conjunction with the Alchemistry.org instructions.

But it needs to be updated a bit more . . .

On Thu, Sep 19, 2013 at 3:38 AM, hsp85  wrote:
> Actually,
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/
> there are two different manuals - one about free energy calculation and
> other about protein ligand complexes.
>
> This page is also can be helpfull
> http://www.alchemistry.org/wiki/Category:Free_Energy_How-to%27s
>
> Sergey Filkin
>
> --
> View this message in context: 
> http://gromacs.5086.x6.nabble.com/Need-protein-ligand-free-energy-calculation-tutorial-tp5011299p5011302.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
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[gmx-users] MPI runs on a local computer

[Xu, Jianqing]

Dear all,

I am learning the parallelization issues from the instructions on Gromacs 
website. I guess I got a rough understanding of MPI, thread-MPI, OpenMP. But I 
hope to get some advice about a correct way to run jobs.

Say I have a local desktop having 16 cores. If I just want to run jobs on one 
computer or a single node (but multiple cores), I understand that I don't have 
to install and use OpenMPI, as Gromacs has its own thread-MPI included already 
and it should be good enough to run jobs on one machine. However, for some 
reasons, OpenMPI has already been installed on my machine, and I compiled 
Gromacs with it by using the flag: "-DGMX_MPI=ON". My questions are:


1.   Can I still use this executable (mdrun_mpi, built with OpenMPI 
library) to run multi-core jobs on my local desktop? Or the default Thread-MPI 
is actually a better option for a single computer or single node (but 
multi-cores) for whatever reasons?

2.   Assuming I can still use this executable, let's say I want to use half 
of the cores (8 cores) on my machine to run a job,

mpirun -np 8 mdrun_mpi -v -deffnm md

a). Since I am not using all the cores, do I still need to "lock" the physical 
cores to use for better performance? Something like "-nt" for Thread-MPI? Or it 
is not necessary?

b). For running jobs on a local desktop, or single node having ...  say 16 
cores, or even 64 cores, should I turn off the "separate PME nodes" (-npme 0)? 
Or it is better to leave as is?

3.   If I want to run two different projects on my local desktop, say one 
project takes 8 cores, the other takes 4 cores (assuming I have enough memory), 
I just submit the jobs twice on my desktop:

nohup mpirun -np 8 mdrun_mpi -v -deffnm md1 >& log1&

nohup mpirun -np 4 mdrun_mpi -v -deffnm md2 >& log2 &

Will this be acceptable ? Will two jobs be competing the resource and 
eventually affect the performance?

Sorry for so many detailed questions, but your help on this will be highly 
appreciated!

Thanks a lot,

Jianqing



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Re: [gmx-users] performance issue with the parallel implementation of gromacs

[ashutosh srivastava]

Thank you Carsten

Will surely try out the suggestions and get back to you


On Thu, Sep 19, 2013 at 1:52 PM, Carsten Kutzner  wrote:

> Hi,
>
> make a scaling test and run on a single node only at first. So you can
> estimate what performance you can at most expect when going to more nodes.
>
> On a single node, you can also run with Gromacs' thread-MPI, thus
> eliminating the possibility that something with your MPI is wrong.
>
> There are lots of reasons why your parallel performance could be bad.
> Can you check that actually the Infiniband interconnect is used and
> not the Ethernet? It could also be that a single process is still
> running on any of your cores and eating up CPU time. Or maybe the
> pinning of threads to cores is not correct (what does md.log say
> about that?).
>
> Just a few ideas.
>
> Good luck!
>
> Carsten
>
>
> On Sep 19, 2013, at 8:07 AM, ashutosh srivastava 
> wrote:
>
> > Hi
> >
> > I have been trying to run simulation on a cluster consisting of 24 nodes
> > Intel(R) Xeon(R) CPU X5670 @ 2.93GHz. Each node has 12 processors and
> they
> > are connected via 1Gbit Ethernet and Infiniband interconnect. The batch
> > system is TORQUE. However due to some issues with the parallel queue I
> have
> > been trying to run the simulations directly on the cluster using mpdboot
> > and mpirun.
> > Following is the mdp.out file that I am using for simulation
> > ; VARIOUS PREPROCESSING OPTIONS
> > ; Preprocessor information: use cpp syntax.
> > ; e.g.: -I/home/joe/doe -I/home/mary/roe
> > include  =
> > ; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case
> sensitive)
> > define   = -DPOSRES
> >
> > ; RUN CONTROL PARAMETERS
> > integrator   = md
> > ; Start time and timestep in ps
> > tinit= 0
> > dt   = 0.002
> > nsteps   = 25
> > ; For exact run continuation or redoing part of a run
> > init-step= 0
> > ; Part index is updated automatically on checkpointing (keeps files
> > separate)
> > simulation-part  = 1
> > ; mode for center of mass motion removal
> > comm-mode= Linear
> > ; number of steps for center of mass motion removal
> > nstcomm  = 100
> > ; group(s) for center of mass motion removal
> > comm-grps=
> >
> > ; LANGEVIN DYNAMICS OPTIONS
> > ; Friction coefficient (amu/ps) and random seed
> > bd-fric  = 0
> > ld-seed  = 1993
> >
> > ; ENERGY MINIMIZATION OPTIONS
> > ; Force tolerance and initial step-size
> > emtol= 10
> > emstep   = 0.01
> > ; Max number of iterations in relax-shells
> > niter= 20
> > ; Step size (ps^2) for minimization of flexible constraints
> > fcstep   = 0
> > ; Frequency of steepest descents steps when doing CG
> > nstcgsteep   = 1000
> > nbfgscorr= 10
> >
> > ; TEST PARTICLE INSERTION OPTIONS
> > rtpi = 0.05
> >
> > ; OUTPUT CONTROL OPTIONS
> > ; Output frequency for coords (x), velocities (v) and forces (f)
> > nstxout  = 100
> > nstvout  = 100
> > nstfout  = 0
> > ; Output frequency for energies to log file and energy file
> > nstlog   = 100
> > nstcalcenergy= 100
> > nstenergy= 100
> > ; Output frequency and precision for .xtc file
> > nstxtcout= 0
> > xtc-precision= 1000
> > ; This selects the subset of atoms for the .xtc file. You can
> > ; select multiple groups. By default all atoms will be written.
> > xtc-grps =
> > ; Selection of energy groups
> > energygrps   =
> >
> > ; NEIGHBORSEARCHING PARAMETERS
> > ; cut-off scheme (group: using charge groups, Verlet: particle based
> > cut-offs)
> > cutoff-scheme= Group
> > ; nblist update frequency
> > nstlist  = 5
> > ; ns algorithm (simple or grid)
> > ns_type  = grid
> > ; Periodic boundary conditions: xyz, no, xy
> > pbc  = xyz
> > periodic-molecules   = no
> > ; Allowed energy drift due to the Verlet buffer in kJ/mol/ps per atom,
> > ; a value of -1 means: use rlist
> > verlet-buffer-drift  = 0.005
> > ; nblist cut-off
> > rlist= 1.0
> > ; long-range cut-off for switched potentials
> > rlistlong= -1
> > nstcalclr= -1
> >
> > ; OPTIONS FOR ELECTROSTATICS AND VDW
> > ; Method for doing electrostatics
> > coulombtype  = PME
> > coulomb-modifier = Potential-shift-Verlet
> > rcoulomb-switch  = 0
> > rcoulomb = 1.0
> > ; Relative dielectric constant for the medium and the reaction field
> > epsilon-r= 1
> > epsilon-rf   = 0
> > ; Method for doing Van der Waals
> > vdw-type = Cut-off
> > vdw-modifier = Potential

Re: [gmx-users] protein unfolding in water

[Justin Lemkul]

On 9/19/13 10:12 AM, fatemeh ramezani wrote:

dear users

I'm studying gold nano-particle effect on one of the blood protein stability 
and structure. one time I simulated the protein in the presence of  the gold 
nanoparticle and once without nanoparticles.

when I simulated protein alone in water, I expected the protein to remain 
stable but protein RMSD, gyration,dssp and  graphs show protein structure 
is changing and protein helices are opening during the simulation.

  Thus, I can not study nanoparticle interaction effect on the protein 
structural changes , because the structural changes also observed  in the 
absence of nanoparticle.
I think there is a problem. What is the solution you offer me? What is the 
problem?



If the model does not reflect reality, that suggests a deficiency in the force 
field, run settings, or system setup.  Since you've told us nothing about how 
you're doing the simulations, there's little advice anyone can offer.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] Problem with http://www.gromacs.org/Documentation/Tutorials page

[Justin Lemkul]

On 9/19/13 10:38 AM, Ray Sheppard wrote:

Hello,
   On the page sited above,  it says:


  General GROMACS Use

  * A step-by-step demo and several simple examples are available in the
share/tutor subdirectory of your GROMACS installation.

However, In the tarfile for version 4.6.3, the directories under "share" are:

rsheppar@login1:/N/dc/projects/ray/br2/testdir/gromacs-4.6.3/share> ls -l
total 36
-rw-r-  1 rsheppar hpc  1922 Jul  5 09:52 CMakeLists.txt
-rw-r-  1 rsheppar hpc79 Jul  5 09:52 README.tutor
-rw-r-  1 rsheppar hpc 13084 Jul  5 09:52 README_FreeEnergyModifications.txt
drwxr-x---  4 rsheppar hpc  4096 Jul  5 10:06 html
drwxr-x---  3 rsheppar hpc  4096 Jul  5 10:06 template
drwxr-x--- 21 rsheppar hpc  4096 Jul  5 10:06 top

Opening README.tutor only points back to the WWW page I started with.  I only
want a simple, idiot test to verify the operation of mdrun in parallel.  Have
the included tutorials been dropped or moved?  Could someone please edit the web
page to fit the current structure?  Thank you.


The "built-in" tutorial was removed because it was wildly outdated and not 
particularly useful (and also not completely fool-proof).  I will remove this 
reference from the web page.


For a straightforward test, it should be very easy to build a simple box of 
water of arbitrary size to do a few runs.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] Problem with http://www.gromacs.org/Documentation/Tutorials page

[Ray Sheppard]

Hello,
  On the page sited above,  it says:


 General GROMACS Use

 * A step-by-step demo and several simple examples are available in the
   share/tutor subdirectory of your GROMACS installation.

However, In the tarfile for version 4.6.3, the directories under "share" 
are:


rsheppar@login1:/N/dc/projects/ray/br2/testdir/gromacs-4.6.3/share> ls -l
total 36
-rw-r-  1 rsheppar hpc  1922 Jul  5 09:52 CMakeLists.txt
-rw-r-  1 rsheppar hpc79 Jul  5 09:52 README.tutor
-rw-r-  1 rsheppar hpc 13084 Jul  5 09:52 
README_FreeEnergyModifications.txt

drwxr-x---  4 rsheppar hpc  4096 Jul  5 10:06 html
drwxr-x---  3 rsheppar hpc  4096 Jul  5 10:06 template
drwxr-x--- 21 rsheppar hpc  4096 Jul  5 10:06 top

Opening README.tutor only points back to the WWW page I started with.  I 
only want a simple, idiot test to verify the operation of mdrun in 
parallel.  Have the included tutorials been dropped or moved?  Could 
someone please edit the web page to fit the current structure?  Thank you.

Ray


--
 Respectfully,
   Ray Sheppard
   rshep...@iu.edu
   http://rt.uits.iu.edu/systems/SciAPT
   317-274-0016

   Principal Analyst
   Senior Technical Lead
   Scientific Applications and Performance Tuning
   Research Technologies
   University Information Technological Services
   IUPUI campus
   Indiana University

   My "pithy" saying:  Science is the art of translating the world
   into language. Unfortunately, that language is mathematics.
   Bumper sticker wisdom: Make it idiot-proof and they will make a
   better idiot.

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Re: [gmx-users] modify nsteps in an existing tpr file

[Guanglei Cui]

Thanks, Mark.

Just compiled gmx 4.0.5 and created tpr with the 'published' topology file.
Ver. 4.0.5 seems to be the version that was used to create the 'published'
tpr file. The only differences now that matter are these c6 and c12 terms.

Is there any mdp options that may change how c6 and c12 are calculated? I
see this ndelta from gmxdump, regardless the versions, but I can't seem to
map it to an mdp option from the manual.



On Thu, Sep 19, 2013 at 6:24 AM, Mark Abraham wrote:

> Indeed - your question was fair, and no undue criticism pertained! :-)
> If you are trying to reproduce something, you must expect .tpr
> differences between 4.0.x and 4.6.y. I illustrated the change that has
> taken place in how VDW parameters are used internally in 4.6, and how
> that is distinct from the (presumably) unchanged description of those
> parameters. How and where to document this kind of thing so that
> people who need it can find it and those who don't need it don't drown
> in paper is an impossible problem!
>
> Cheers,
>
> Mark
>
> On Wed, Sep 18, 2013 at 8:34 PM, Guanglei Cui
>  wrote:
> > It is only a simple question, not a criticism of any kind. I'm sure there
> > may be perfect reasons to choose one implementation over another. To
> > someone who is not familiar with the history of gmx development, it is
> > something to be aware of. That's all.
> >
> >
> > On Wed, Sep 18, 2013 at 4:56 PM, Mark Abraham  >wrote:
> >
> >> Implementation and description of a model physics are two different
> >> things. You could compute KE of a particle with 0.5 * m * v^2, but if
> >> the mass is used nowhere else, why wouldn't you pre-multiply the mass
> >> by 0.5?
> >>
> >> Mark
> >>
> >> On Wed, Sep 18, 2013 at 4:31 PM, Guanglei Cui
> >>  wrote:
> >> > hmm, does that mean the gmx force field file format or specifications
> are
> >> > not backward compatible?
> >> >
> >> >
> >> > On Wed, Sep 18, 2013 at 4:08 PM, Mark Abraham <
> mark.j.abra...@gmail.com
> >> >wrote:
> >> >
> >> >> There are technical differences between versions about how the VDW
> >> >> parameters are computed. You should not expect .tpr equivalence
> >> >> between minor version changes such as 4.0 and 4.6. You need to
> compile
> >> >> a 4.0.x grompp to see if your setup is equivalent, but having done so
> >> >> you should be able to use the same inputs to 4.6 grompp and get a
> >> >> correct simulation with 4.6 mdrun.
> >> >>
> >> >> Mark
> >> >>
> >> >> On Wed, Sep 18, 2013 at 1:55 PM, Guanglei Cui
> >> >>  wrote:
> >> >> > Thanks. gmxcheck is quite helpful. Here is part of the output. It
> >> turns
> >> >> out
> >> >> > the difference is mainly in the force field parameters, which
> >> indicates
> >> >> the
> >> >> > top file provided may not be the one used to produce the tpr file.
> >> >> Perhaps
> >> >> > it is best to contact the authors, unless the difference is due to
> >> >> certain
> >> >> > changes between gmx 4.0.x and gmx 4.6.3.
> >> >> >
> >> >> > inputrec->nsteps (5000 - 5000)
> >> >> > inputrec->nstcalclr (5 - 0)
> >> >> > inputrec->nstdhdl (1 - 50)
> >> >> > inputrec->fepvals->init_fep_state ( 0.0e+00 -
> >> -1.0e+00)
> >> >> > inputrec->fepvals->lambda_neighbors[1] (0 - 1)
> >> >> > inputrec->fepvals->sc_power (0 - 1)
> >> >> > inputrec->dihre_fc (1.00e+03 - 0.00e+00)
> >> >> > inputrec->grpopts.ngtc (4 - 1)
> >> >> > inputrec->grpopts.ngener (4 - 1)
> >> >> > inputrec->grpopts.nrdf[ 0] (8.610900e+04 - 2.136210e+05)
> >> >> > idef->iparam[12]1: c6= 4.23112651e-03, c12= 4.76949208e-06
> >> >> > idef->iparam[12]2: c6= 4.68938737e-08, c12= 1.15147106e-12
> >> >> > idef->iparam[54]1: c6= 4.58155479e-03, c12= 4.48611081e-06
> >> >> > idef->iparam[54]2: c6= 4.46544206e-08, c12= 8.37594751e-13
> >> >> > idef->iparam[82]1: c6= 3.75142763e-03, c12= 4.22875655e-06
> >> >> > idef->iparam[82]2: c6= 4.15773336e-08, c12= 1.02092445e-12
> >> >> > idef->iparam[96]1: c6= 3.8381e-03, c12= 2.83264171e-06
> >> >> > idef->iparam[96]2: c6= 2.83739432e-08, c12= 3.04270091e-13
> >> >> > idef->iparam[124]1: c6= 4.26879199e-03, c12= 3.50070763e-06
> >> >> > idef->iparam[124]2: c6= 3.50897622e-08, c12= 4.64908439e-13
> >> >> > idef->iparam[152]1: c6= 3.59375845e-03, c12= 2.76020933e-06
> >> >> > idef->iparam[152]2: c6= 2.76677472e-08, c12= 3.21553060e-13
> >> >> > idef->iparam[166]1: c6= 7.79988989e-03, c12= 1.19875567e-05
> >> >> > idef->iparam[166]2: c6= 1.12529349e-07, c12= 4.90395051e-12
> >> >> > idef->iparam[168]1: c6= 4.23112651e-03, c12= 4.76949208e-06
> >> >> > idef->iparam[168]2: c6= 4.68938737e-08, c12= 1.15147106e-12
> >> >> > idef->iparam[171]1: c6= 4.58155479e-03, c12= 4.48611081e-06
> >> >> > idef->iparam[171]2: c6= 4.46544206e-08, c12= 8.37594751e-13
> >> >> > idef->iparam[173]1: c6= 3.75142763e-03, c12= 4.22875655e-06
> >> >> > idef->iparam[173]2: c6= 4.15773336e-08, c12= 1.02092445e-12
> >> >> > idef->iparam[174]1: c6= 3.8381e-03, c12= 2.83264171e-06
> >> >> > idef->iparam[174]2: c6= 2.83739432e-08, c12= 3.0

[gmx-users] protein unfolding in water

[fatemeh ramezani]

dear users

I'm studying gold nano-particle effect on one of the blood protein stability 
and structure. one time I simulated the protein in the presence of  the gold 
nanoparticle and once without nanoparticles.

when I simulated protein alone in water, I expected the protein to remain 
stable but protein RMSD, gyration,dssp and  graphs show protein structure 
is changing and protein helices are opening during the simulation.  

 Thus, I can not study nanoparticle interaction effect on the protein 
structural changes , because the structural changes also observed  in the 
absence of nanoparticle.
I think there is a problem. What is the solution you offer me? What is the 
problem? 

sincerely

Fatemeh Ramezani
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Re: [gmx-users] Re: grompp for minimization: note & warning

[Tsjerk Wassenaar]

Hi Shahab,

You edited the .gro file, but you made an error. So you have to read the
manual to understand the file format and then see where and how your edited
file doesn't match.

Cheers,

Tsjerk


On Thu, Sep 19, 2013 at 5:00 PM, shahab shariati
wrote:

> Dear Tsjerk
>
> Thanks for your consideration.
>
> I ignored Warning 1.
>
> > WARNING 1 [file topol.top, line 32]:
> >   3632 non-matching atom names
> >   atom names from topol.top will be used
> >   atom names from system.gro will be ignored
>
> Based on your suggestion, I checked non-matching
> atom names between topol.top and system.gro files.
>
> I corrected system.gro file accordance with topol.top file.
>
> I did this work very carefully. I was watchful to not
> disturb the format of the system.gro file, so that when I saw
> system gro file (before and after the correction) by an editor
> program, both of them were same.
>
> But, when I use grompp, I encountered with:
>
> Fatal error:
> Something is wrong in the coordinate formatting of file sys.gro.
> Note that gro is fixed format (see the manual).
>
> How to solve this problem?
>
> Any help will highly appreciated.
>
> Best wishes for you.
> --
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>



-- 
Tsjerk A. Wassenaar, Ph.D.
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[gmx-users] Re: grompp for minimization: note & warning

[shahab shariati]

Dear Tsjerk

Thanks for your consideration.

I ignored Warning 1.

> WARNING 1 [file topol.top, line 32]:
>   3632 non-matching atom names
>   atom names from topol.top will be used
>   atom names from system.gro will be ignored

Based on your suggestion, I checked non-matching
atom names between topol.top and system.gro files.

I corrected system.gro file accordance with topol.top file.

I did this work very carefully. I was watchful to not
disturb the format of the system.gro file, so that when I saw
system gro file (before and after the correction) by an editor
program, both of them were same.

But, when I use grompp, I encountered with:

Fatal error:
Something is wrong in the coordinate formatting of file sys.gro.
Note that gro is fixed format (see the manual).

How to solve this problem?

Any help will highly appreciated.

Best wishes for you.
-- 
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Re: [gmx-users] Regarding g_sgangle index file

[Venkat Reddy]

Dear Sir,
The tool "gmx gangle" is wonderful. The additional options are very
flexible and easy to use.
@Teemu Murtola: Are there any modifications to the other gmx tools? (eg:
rdf calculation with dynamic selection...etc). I am trying to explore the
new version.

Thank you


On Tue, Sep 17, 2013 at 11:31 PM, Teemu Murtola wrote:

> Hello,
>
> Please keep correspondence on the list so that others may benefit from it,
> and you don't need to wait for some particular person to respond.
>
> On Tue, Sep 17, 2013 at 1:24 PM, Venkat Reddy  wrote:
> >
> > On Tue, Sep 17, 2013 at 12:38 AM, Teemu Murtola  >
> >>  wrote:
> >>
> >>> version (from the git master branch), you can use a much more powerful
> >>> 'gmx
> >>> gangle' tool, which can calculate multiple angles in one go.
> >>>
> >>
> > I have installed the "gromacs-master" version from GIT, but I couldn't
> see
> > any changes between the old g_sgangle and the current one. Is the new
> tool
> > underway in development?
> >
>
> Try "gmx gangle -h" per my original suggestion. The g_sgangle tool hasn't
> been touched.
>
> Best regards,
> Teemu
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>



-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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Re: [gmx-users] forcefield and setting

[Justin Lemkul]

On 9/19/13 11:59 AM, fatemeh ramezani wrote:



  Dear Justin
I used gromacs OPLSAA forcefield for simulation of protein and TIP3P model for 
water.

em.mdp file:
title   =  n.pdb
cpp =  /lib/cpp
define  =  -DFLEXIBLE
constraints =  none
integrator  =  steep
nsteps  =  4
constraint_algorithm  =
shake_tol   = 0.0001
nstenergy   =  10
nstxtcout   =  1
nstlist =  5
nstcomm =  1
ns_type =  grid
rlist   =  1
coulombtype =  PME
rcoulomb=  1
rvdw=  1
fourierspacing  =  0.12
fourier_nx  =  0
fourier_ny  =  0
fourier_nz  =  0
pme_order   =  8
ewald_rtol  =  1e-5
optimize_fft=  yes
emtol   =  1000.0
emstep  =  0.01

md.mdp file:
title   =  n.pdb restraining
cpp =  /lib/cpp
constraints =  none
integrator  =  md
dt  =  0.0008
nsteps  =  2500
nstcomm =  10
comm_mode   =
nstxout =  250
nstvout =  1000
nstfout =  0
nstlog  =  10
nstenergy   =  10
nstlist =  10
ns_type =  grid
rlist   =  0.9
coulombtype =  PME
rcoulomb=  0.9
rcoulomb-switch =  1
rvdw=  0.5
vdwtype =  shift


Your van der Waals settings make no sense.  I strongly suspect that this is 
inducing very nasty artifacts.


-Justin


;rvdw-switch =  0.6
fourierspacing  =  0.12
fourier_nx  =  0
fourier_ny  =  0
fourier_nz  =  0
pme_order   =  6
ewald_rtol  =  1e-5
optimize_fft=  yes


; Berendsen temperature coupling is on in three groups
Tcoupl  =  V-rescale
tau_t   =  0.1   0.1
tc-grps=  Protein   Non-Protein
ref_t   =  300   300
; Pressure coupling is  on
;Pcoupl  =  berendsen
Pcoupl  =  no
Pcoupltype =  isotropic
tau_p   =  0.5
compressibility =  4.5e-5
ref_p   =  1.0
; Generate velocites is on at 300 K.
gen_vel =  yes
gen_temp=  300.0
gen_seed=  173529
energygrps  = Protein  Sol



Fatemeh Ramezani



--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] Charmm 36 forcefield with verlet cut-off scheme

[akk5r]

Hey All, 

I am running a simulation of a POPC bilayer in water using a Charmm 36
forcefield. I am having trouble using cutoff-scheme=Verlet in my nvt
equilibration. 

My .mdp file is as follows: 

title= OPLS Lysozyme NVT 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  = 0 ; save coordinates every 0.2 ps 
nstvout  = 0 ; save velocities every 0.2 ps 
nstenergy   = 0  ; save energies every 0.2 ps 
nstlog   = 0 ; update log file every 0.2 ps 
; Bond parameters 
continuation= no ; first dynamics run 
constraint_algorithm = lincs; holonomic constraints 
constraints = all-bonds ; all bonds (even heavy atom-H bonds) 
constrained 
lincs_iter  = 1  ; accuracy of LINCS 
lincs_order = 4  ; also related to accuracy 
; Neighborsearching 
ns_type  = grid  ; search neighboring grid cells 
nstlist  = 5 ; 10 fs 
rlist= 1.2   ; short-range neighborlist cutoff (in nm) 
rcoulomb= 1.2; short-range electrostatic cutoff (in nm) 
rvdw = 1.2   ; short-range van der Waals cutoff (in nm) 
rcoulomb-switch  = 0 
rvdw-switch  = 1.0 
; long-range cut-off for switched potentials 
rlistlong= 1.4 
; Electrostatics 
coulombtype = PME; Particle Mesh Ewald for long-range electrostatics 
pme_order   = 4  ; cubic interpolation 
fourierspacing  = 0.16   ; grid spacing for FFT 
; Relative dielectric constant for the medium and the reaction field 
epsilon_r= 1 
epsilon_rf   = 1 
; Temperature coupling is on 
tcoupl   = V-rescale; modified Berendsen thermostat 
tc-grps  = POPC SOL ; two coupling groups - more accurate 
tau_t= 0.1  0.1 ; time constant, in ps 
ref_t= 300 300  ; reference temperature, one for each group, in K 
; Pressure coupling is off 
pcoupl   = no ; no pressure coupling in NVT 
; Periodic boundary conditions 
pbc  = xyz   ; 3-D PBC 
; Dispersion correction 
DispCorr= No; account for cut-off vdW scheme 
; Method for doing Van der Waals 
vdw-type = switch 
; Velocity generation 
gen_vel  = yes   ; assign velocities from Maxwell distribution 
gen_temp= 300; temperature for Maxwell distribution 
gen_seed= -1 ; generate a random seed 
cutoff-scheme   = Verlet 

*Here is the output when I run grompp to make the .tpr file:*

grompp -f nvt.mdp -c em_POPC.gro -p topol.top -o nvt.tpr 

ERROR 1 [file nvt.mdp]: 
  With Verlet lists only cut-off LJ interactions are supported 


NOTE 1 [file nvt.mdp]: 
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 
  that with the Verlet scheme, nstlist has no effect on the accuracy of 
  your simulation. 


NOTE 2 [file nvt.mdp]: 
  The switch/shift interaction settings are just for compatibility; you 
  will get better performance from applying potential modifiers to your 
  interactions! 


Generated 21528 of the 21528 non-bonded parameter combinations 
Generating 1-4 interactions: fudge = 1 
Generated 18355 of the 21528 1-4 parameter combinations 
Excluding 3 bonded neighbours molecule type 'POPC' 
turning all bonds into constraints... 
Excluding 2 bonded neighbours molecule type 'SOL' 
turning all bonds into constraints... 
Setting gen_seed to 7358 
Velocities were taken from a Maxwell distribution at 300 K 
Removing all charge groups because cutoff-scheme=Verlet 

There were 2 notes 

--- 
Program grompp, VERSION 4.6.1 
Source code file: /home/ali/Downloads/gromacs-4.6.1/src/kernel/grompp.c,
line: 1593 

Fatal error: 
There was 1 error in input file(s) 
For more information and tips for troubleshooting, please check the GROMACS 
website at http://www.gromacs.org/Documentation/Errors
--- 

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[gmx-users] forcefield and setting

[fatemeh ramezani]

 Dear Justin
I used gromacs OPLSAA forcefield for simulation of protein and TIP3P model for 
water.

em.mdp file:
title   =  n.pdb
cpp =  /lib/cpp
define  =  -DFLEXIBLE
constraints =  none
integrator  =  steep
nsteps  =  4
constraint_algorithm  =
shake_tol   = 0.0001
nstenergy   =  10
nstxtcout   =  1
nstlist =  5
nstcomm =  1
ns_type =  grid
rlist   =  1
coulombtype =  PME
rcoulomb    =  1
rvdw    =  1
fourierspacing  =  0.12
fourier_nx  =  0
fourier_ny  =  0
fourier_nz  =  0
pme_order   =  8
ewald_rtol  =  1e-5
optimize_fft    =  yes
emtol   =  1000.0
emstep  =  0.01

md.mdp file:
title   =  n.pdb restraining
cpp =  /lib/cpp
constraints =  none
integrator  =  md 
dt  =  0.0008
nsteps  =  2500
nstcomm =  10
comm_mode   =  
nstxout =  250
nstvout =  1000
nstfout =  0
nstlog  =  10
nstenergy   =  10
nstlist =  10
ns_type =  grid
rlist   =  0.9
coulombtype =  PME
rcoulomb    =  0.9
rcoulomb-switch =  1
rvdw    =  0.5
vdwtype =  shift
;rvdw-switch =  0.6
fourierspacing  =  0.12
fourier_nx  =  0
fourier_ny  =  0
fourier_nz  =  0
pme_order   =  6
ewald_rtol  =  1e-5
optimize_fft    =  yes
  

; Berendsen temperature coupling is on in three groups
Tcoupl  =  V-rescale
tau_t   =  0.1   0.1
tc-grps            =  Protein   Non-Protein
ref_t   =  300   300
; Pressure coupling is  on
;Pcoupl  =  berendsen
Pcoupl  =  no
Pcoupltype =  isotropic
tau_p   =  0.5
compressibility =  4.5e-5
ref_p   =  1.0
; Generate velocites is on at 300 K.
gen_vel =  yes
gen_temp    =  300.0
gen_seed    =  173529
energygrps  = Protein  Sol 



Fatemeh Ramezani
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[gmx-users] SDFs memory allocation error

[Marta Batista]

Hi, 

I am trying to perform SDFs using g_spatial tool from Gromacs.
I did all steps, recommended and indicated in Gromacs' manual,

1. Use make_ndx to create a group containing the atoms around which you want 
the SDF
2. trjconv -s a.tpr -f a.xtc -o b.xtc -center tric -ur compact -pbc none
3. trjconv -s a.tpr -f b.xtc -o c.xtc -fit rot+trans
4. run g_spatial on the .xtc output of step #3.

 but no matter the atoms of my systems that I choose to see in the SDF, I keep 
having the problem:

"Reading frame   0 time0.000   Memory allocation error"

As in the manual, they say that this could hapen and we should increase the 
-nab value. I did it, and I keep having this problem

Can anyone help me, to solve this problem?

Thank you.




Marta Batista

PhD student
Department of Chemistry
Campus Universitário de Santiago
University of Aveiro
batist...@ua.pt
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Re: [gmx-users] Charmm 36 forcefield with verlet cut-off scheme

[Justin Lemkul]

On 9/19/13 2:21 PM, akk5r wrote:

Hey All,

I am running a simulation of a POPC bilayer in water using a Charmm 36
forcefield. I am having trouble using cutoff-scheme=Verlet in my nvt
equilibration.

My .mdp file is as follows:

title= OPLS Lysozyme NVT 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  = 0 ; save coordinates every 0.2 ps
nstvout  = 0 ; save velocities every 0.2 ps
nstenergy   = 0  ; save energies every 0.2 ps
nstlog   = 0 ; update log file every 0.2 ps
; Bond parameters
continuation= no ; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds) 
constrained
lincs_iter  = 1  ; accuracy of LINCS
lincs_order = 4  ; also related to accuracy
; Neighborsearching
ns_type  = grid  ; search neighboring grid cells
nstlist  = 5 ; 10 fs
rlist= 1.2   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.2; short-range electrostatic cutoff (in nm)
rvdw = 1.2   ; short-range van der Waals cutoff (in nm)
rcoulomb-switch  = 0
rvdw-switch  = 1.0
; long-range cut-off for switched potentials
rlistlong= 1.4
; Electrostatics
coulombtype = PME; Particle Mesh Ewald for long-range electrostatics
pme_order   = 4  ; cubic interpolation
fourierspacing  = 0.16   ; grid spacing for FFT
; Relative dielectric constant for the medium and the reaction field
epsilon_r= 1
epsilon_rf   = 1
; Temperature coupling is on
tcoupl   = V-rescale; modified Berendsen thermostat
tc-grps  = POPC SOL ; two coupling groups - more accurate
tau_t= 0.1  0.1 ; time constant, in ps
ref_t= 300 300  ; reference temperature, one for each group, in K
; Pressure coupling is off
pcoupl   = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc  = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= No; account for cut-off vdW scheme
; Method for doing Van der Waals
vdw-type = switch
; Velocity generation
gen_vel  = yes   ; assign velocities from Maxwell distribution
gen_temp= 300; temperature for Maxwell distribution
gen_seed= -1 ; generate a random seed
cutoff-scheme   = Verlet

*Here is the output when I run grompp to make the .tpr file:*

grompp -f nvt.mdp -c em_POPC.gro -p topol.top -o nvt.tpr

ERROR 1 [file nvt.mdp]:
   With Verlet lists only cut-off LJ interactions are supported


NOTE 1 [file nvt.mdp]:
   With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
   that with the Verlet scheme, nstlist has no effect on the accuracy of
   your simulation.


NOTE 2 [file nvt.mdp]:
   The switch/shift interaction settings are just for compatibility; you
   will get better performance from applying potential modifiers to your
   interactions!


Generated 21528 of the 21528 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 18355 of the 21528 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'POPC'
turning all bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning all bonds into constraints...
Setting gen_seed to 7358
Velocities were taken from a Maxwell distribution at 300 K
Removing all charge groups because cutoff-scheme=Verlet

There were 2 notes

---
Program grompp, VERSION 4.6.1
Source code file: /home/ali/Downloads/gromacs-4.6.1/src/kernel/grompp.c,
line: 1593

Fatal error:
There was 1 error in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---



As the error message says, with "cutoff-scheme = Verlet" you must use "vdwtype = 
cutoff."  The notes above suggest reasonable methods for implementing switched 
interactions.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] SDFs memory allocation error

[Justin Lemkul]

On 9/19/13 2:56 PM, Marta Batista wrote:


Hi,

I am trying to perform SDFs using g_spatial tool from Gromacs.
I did all steps, recommended and indicated in Gromacs' manual,

1. Use make_ndx to create a group containing the atoms around which you want 
the SDF
2. trjconv -s a.tpr -f a.xtc -o b.xtc -center tric -ur compact -pbc none
3. trjconv -s a.tpr -f b.xtc -o c.xtc -fit rot+trans
4. run g_spatial on the .xtc output of step #3.

  but no matter the atoms of my systems that I choose to see in the SDF, I keep 
having the problem:

"Reading frame   0 time0.000   Memory allocation error"

As in the manual, they say that this could hapen and we should increase the 
-nab value. I did it, and I keep having this problem

Can anyone help me, to solve this problem?



How large is the group for which you are trying to calculate an SDF (how many 
atoms)?  As I recall, g_spatial requires a lot of memory, so if you have a lot 
of atoms, it may simply not be possible depending on your available memory.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] changing atom types versus adding dihedrals to atom types

[Rafael I. Silverman y de la Vega]

Hmm, I will have to do some more controls then, but I  prob dont have time
to do them till after quals this fall...
You mention Hartree-Fock methods, does this mean that you disfavor DFT for
some reason for this purpose?


On Tue, Sep 17, 2013 at 5:40 PM, Justin Lemkul  wrote:

>
>
> On 9/17/13 8:18 PM, Rafael I. Silverman y de la Vega wrote:
>
>> Can you give some examples of how these verifications are  different for
>> different force fields? It doesnt seem like verifying takes that much
>> time,
>> but a theorist prof in my department told me not to worry as long as my
>> system doesnt blow up...
>>
>
> IMHO simply not blowing up tells you nothing.  I can show you a dozen
> simulations that don't blow up that have terrible small molecule topologies
> that produce bad results.
>
> Parametrization methods and validation procedures are defined in the
> literature and one could easily fill a book chapter (or more) on such
> topics, so I will not go into it in an email.  You may have to go back
> several years (or even decades) in the literature to get the full story.
>
>
>  And what do you mean "thourough parametrization?
>>
>
> Most people hope for a simple, one-shot step they can take to parametrize
> a small molecule.  There are numerous "black box" methods out there, some
> good and some bad.  I advise people to be thorough in terms of what the
> force field requires and what their chemical knowledge tells them.  For
> instance, for water interactions in CHARMM, HF/6-31G* works well for most
> compounds, unless sulfur is involved, in which case we need to do a more
> expensive MP2/6-31G* calculation.  You can get an OK result for everything
> with HF, but it's not sufficiently accurate in all cases.
>
>
>  I parametrized flavin mononucleotide using amber99sb-ildn, I used existing
>> atomtypes in the force field, but I added partial atomic charges based on
>> a
>> decent DFT calculation in orca, and I had to add 2 distance restraints on
>> the delta negatively charged phosphate oxygens to keep them from crashing
>> into the delta positive hydrogen on the same phosphate. Is that thorough
>> in
>> your opinion?
>>
>
> How does it compare with the results of running the molecule through
> antechamber?  Usually GAFF gives a reasonable topology with minimal
> adjustment necessary.  That's one of the benefits of Amber; there are very
> well-defined protocols and a robust general force field for the
> parametrization.
>
> -Justin
>
>
> --
> ==**
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul@outerbanks.umaryland.**edu  | 
> (410)
> 706-7441
>
> ==**
> --
> 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
>
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Re: [gmx-users] changing atom types versus adding dihedrals to atom types

[Rafael I. Silverman y de la Vega]

Sulpher is important, but it is in the apoprotein, not the parametrized
prosthetic group


On Thu, Sep 19, 2013 at 6:51 PM, Rafael I. Silverman y de la Vega <
rsilv...@ucsc.edu> wrote:

> Hmm, I will have to do some more controls then, but I  prob dont have time
> to do them till after quals this fall...
> You mention Hartree-Fock methods, does this mean that you disfavor DFT for
> some reason for this purpose?
>
>
> On Tue, Sep 17, 2013 at 5:40 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 9/17/13 8:18 PM, Rafael I. Silverman y de la Vega wrote:
>>
>>> Can you give some examples of how these verifications are  different for
>>> different force fields? It doesnt seem like verifying takes that much
>>> time,
>>> but a theorist prof in my department told me not to worry as long as my
>>> system doesnt blow up...
>>>
>>
>> IMHO simply not blowing up tells you nothing.  I can show you a dozen
>> simulations that don't blow up that have terrible small molecule topologies
>> that produce bad results.
>>
>> Parametrization methods and validation procedures are defined in the
>> literature and one could easily fill a book chapter (or more) on such
>> topics, so I will not go into it in an email.  You may have to go back
>> several years (or even decades) in the literature to get the full story.
>>
>>
>>  And what do you mean "thourough parametrization?
>>>
>>
>> Most people hope for a simple, one-shot step they can take to parametrize
>> a small molecule.  There are numerous "black box" methods out there, some
>> good and some bad.  I advise people to be thorough in terms of what the
>> force field requires and what their chemical knowledge tells them.  For
>> instance, for water interactions in CHARMM, HF/6-31G* works well for most
>> compounds, unless sulfur is involved, in which case we need to do a more
>> expensive MP2/6-31G* calculation.  You can get an OK result for everything
>> with HF, but it's not sufficiently accurate in all cases.
>>
>>
>>  I parametrized flavin mononucleotide using amber99sb-ildn, I used
>>> existing
>>> atomtypes in the force field, but I added partial atomic charges based
>>> on a
>>> decent DFT calculation in orca, and I had to add 2 distance restraints on
>>> the delta negatively charged phosphate oxygens to keep them from crashing
>>> into the delta positive hydrogen on the same phosphate. Is that thorough
>>> in
>>> your opinion?
>>>
>>
>> How does it compare with the results of running the molecule through
>> antechamber?  Usually GAFF gives a reasonable topology with minimal
>> adjustment necessary.  That's one of the benefits of Amber; there are very
>> well-defined protocols and a robust general force field for the
>> parametrization.
>>
>> -Justin
>>
>>
>> --
>> ==**
>>
>> Justin A. Lemkul, Ph.D.
>> Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul@outerbanks.umaryland.**edu | 
>> (410)
>> 706-7441
>>
>> ==**
>> --
>> 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
>>
>
>
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[gmx-users] Re: Charmm 36 forcefield with verlet cut-off scheme

[akk5r]

Thanks Justin. I was told that the "vdwtype = switch" was an essential
component of running Charmm36. Is that not the case?

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Re: [gmx-users] changing atom types versus adding dihedrals to atom types

[Justin Lemkul]

On 9/19/13 9:51 PM, Rafael I. Silverman y de la Vega wrote:

Sulpher is important, but it is in the apoprotein, not the parametrized
prosthetic group



I only mentioned this as one example where user input and intuition is useful, 
not necessarily to directly comment on anything you are doing.


-Justin



On Thu, Sep 19, 2013 at 6:51 PM, Rafael I. Silverman y de la Vega <
rsilv...@ucsc.edu> wrote:


Hmm, I will have to do some more controls then, but I  prob dont have time
to do them till after quals this fall...
You mention Hartree-Fock methods, does this mean that you disfavor DFT for
some reason for this purpose?


On Tue, Sep 17, 2013 at 5:40 PM, Justin Lemkul  wrote:




On 9/17/13 8:18 PM, Rafael I. Silverman y de la Vega wrote:


Can you give some examples of how these verifications are  different for
different force fields? It doesnt seem like verifying takes that much
time,
but a theorist prof in my department told me not to worry as long as my
system doesnt blow up...



IMHO simply not blowing up tells you nothing.  I can show you a dozen
simulations that don't blow up that have terrible small molecule topologies
that produce bad results.

Parametrization methods and validation procedures are defined in the
literature and one could easily fill a book chapter (or more) on such
topics, so I will not go into it in an email.  You may have to go back
several years (or even decades) in the literature to get the full story.


  And what do you mean "thourough parametrization?




Most people hope for a simple, one-shot step they can take to parametrize
a small molecule.  There are numerous "black box" methods out there, some
good and some bad.  I advise people to be thorough in terms of what the
force field requires and what their chemical knowledge tells them.  For
instance, for water interactions in CHARMM, HF/6-31G* works well for most
compounds, unless sulfur is involved, in which case we need to do a more
expensive MP2/6-31G* calculation.  You can get an OK result for everything
with HF, but it's not sufficiently accurate in all cases.


  I parametrized flavin mononucleotide using amber99sb-ildn, I used

existing
atomtypes in the force field, but I added partial atomic charges based
on a
decent DFT calculation in orca, and I had to add 2 distance restraints on
the delta negatively charged phosphate oxygens to keep them from crashing
into the delta positive hydrogen on the same phosphate. Is that thorough
in
your opinion?



How does it compare with the results of running the molecule through
antechamber?  Usually GAFF gives a reasonable topology with minimal
adjustment necessary.  That's one of the benefits of Amber; there are very
well-defined protocols and a robust general force field for the
parametrization.

-Justin


--
==**

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul@outerbanks.umaryland.**edu | (410)
706-7441

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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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Re: [gmx-users] changing atom types versus adding dihedrals to atom types

[Justin Lemkul]

On 9/19/13 9:51 PM, Rafael I. Silverman y de la Vega wrote:

Hmm, I will have to do some more controls then, but I  prob dont have time
to do them till after quals this fall...
You mention Hartree-Fock methods, does this mean that you disfavor DFT for
some reason for this purpose?



For CHARMM, we use ab initio approaches that have been well documented in the 
literature.  The molecules are all small enough that all the calculations take a 
couple hours or less.


-Justin



On Tue, Sep 17, 2013 at 5:40 PM, Justin Lemkul  wrote:




On 9/17/13 8:18 PM, Rafael I. Silverman y de la Vega wrote:


Can you give some examples of how these verifications are  different for
different force fields? It doesnt seem like verifying takes that much
time,
but a theorist prof in my department told me not to worry as long as my
system doesnt blow up...



IMHO simply not blowing up tells you nothing.  I can show you a dozen
simulations that don't blow up that have terrible small molecule topologies
that produce bad results.

Parametrization methods and validation procedures are defined in the
literature and one could easily fill a book chapter (or more) on such
topics, so I will not go into it in an email.  You may have to go back
several years (or even decades) in the literature to get the full story.


  And what do you mean "thourough parametrization?




Most people hope for a simple, one-shot step they can take to parametrize
a small molecule.  There are numerous "black box" methods out there, some
good and some bad.  I advise people to be thorough in terms of what the
force field requires and what their chemical knowledge tells them.  For
instance, for water interactions in CHARMM, HF/6-31G* works well for most
compounds, unless sulfur is involved, in which case we need to do a more
expensive MP2/6-31G* calculation.  You can get an OK result for everything
with HF, but it's not sufficiently accurate in all cases.


  I parametrized flavin mononucleotide using amber99sb-ildn, I used existing

atomtypes in the force field, but I added partial atomic charges based on
a
decent DFT calculation in orca, and I had to add 2 distance restraints on
the delta negatively charged phosphate oxygens to keep them from crashing
into the delta positive hydrogen on the same phosphate. Is that thorough
in
your opinion?



How does it compare with the results of running the molecule through
antechamber?  Usually GAFF gives a reasonable topology with minimal
adjustment necessary.  That's one of the benefits of Amber; there are very
well-defined protocols and a robust general force field for the
parametrization.

-Justin


--
==**

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul@outerbanks.umaryland.**edu  | (410)
706-7441

==**
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--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] Re: Charmm 36 forcefield with verlet cut-off scheme

[Justin Lemkul]

On 9/19/13 9:55 PM, akk5r wrote:

Thanks Justin. I was told that the "vdwtype = switch" was an essential
component of running Charmm36. Is that not the case?



It is, but I suppose one can achieve a similar effect with the Verlet scheme. 
You can certainly use the traditional CHARMM settings if you use the group 
scheme, instead.  The vdw-modifier setting should give you a comparable result, 
but I have never tried it myself.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] Fatal Error: Residue 'DMP' not found in residue topology database

[Santhosh Kumar Nagarajan]

Hi guys, 
 The error I'm getting is as follows
"All occupancies are one
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomtypes.atp
Atomtype 1
Reading residue database... (oplsaa)
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.rtp
Residue 56
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb
Processing chain 1 'A' (46 atoms, 1 residues)
There are 0 donors and 0 acceptors
There are 0 hydrogen bonds
Warning: Starting residue DMP1 in chain not identified as Protein/RNA/DNA.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully

---
Program pdb2gmx, VERSION 4.5.3
Source code file: resall.c, line: 581

Fatal error:
Residue 'DMP' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---"

And this is the command I used

pdb2gmx -f dmpc.pdb -o processed.gro -water spce -ignh

Force field : OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)

Help me solve this.
Thanks and Regards
Santhosh.


-
Santhosh Kumar Nagarajan
MTech Bioinformatics
SRM University
Chennai
India
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