Re: [gmx-users] minimization for final configuration

[Dr. Vitaly Chaban]

Indeed, it is unlikely that averaged coordinates of certain structure
versus time correspond to something physically meaningful.

How do you average them, by the way? And what for, please?


Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН


On Tue, Sep 30, 2014 at 12:47 PM, Justin Lemkul  wrote:
>
>
> On 9/30/14 3:36 AM, Mahboobeh Eslami wrote:
>>
>> hi GMX users
>> i have simulated the protein-ligand complex by gromacs for 20ns.
>> The average for the final structure of 18 to 20 nanoseconds has been
>> achieved.is minimization for the final average structure required?Sincerely.
>>
>
> An average structure might be totally unphysical.  Energy minimization of an
> unphysical structure leads you to something that is probably useless.  I'd
> suggest doing clustering if you're interested in the predominant
> conformation(s) during a certain time period of the simulation.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA 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
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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Re: [gmx-users] Why should I repeat my simulation?

[Dr. Vitaly Chaban]

And one trivial coin from me...

Not only the random seed for the initial velocity distribution must be
altered, but it is also very good to start from a significantly
different set of coordinates.


Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН


On Sat, Oct 4, 2014 at 11:15 PM, fatemeh ramezani  wrote:
> Dear gmx-users
>
> I performed a MD simulation with gromacs software and after sending my 
> results to a journal, referee said
>
> "Simulations needs to
> be repeated with different initial velocity (seed) to make sure that the
> results are not simulation artifacts.It is needed to ensure that the 
> simulation represents true dynamics
> of the system."
> It is really need to I repeat my simulation (that is very time-consuming 
> process) or you can help me to providea compelling reason for not repeating.
>
> Thanks in advance
>
> Fatemeh Ramezani
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Re: [gmx-users] Use NVT to mimic NVE

[Dr. Vitaly Chaban]

what is it needed for?



Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН


On Fri, Oct 10, 2014 at 7:41 PM, Johnny Lu  wrote:
> Hi.
>
> Is it a good idea to mimic NVE by a NVT simulation with a large temperature
> coupling time constant, to reduce the effect of the thermostat ?
>
> If I use V-rescale thermostat, what artifacts will the simulation get if I
> use a large coupling time (say, 500 ps) and single precision gromacs ?
>
> Thank you.
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Re: [gmx-users] Use NVT to mimic NVE

[Dr. Vitaly Chaban]

I also cannot get why not to just turn off the thermostat...

If energy transfer phenomena are in focus, NVE is an ensemble of
choice, no matter which relaxation constant is used for the T-coupling
algorithm.


Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН


On Sat, Oct 11, 2014 at 6:32 PM, Antonio Baptista  wrote:
> Then, run true NVE, for the reasons we already pointed.
>
> On Sat, 11 Oct 2014, Johnny Lu wrote:
>
>> For dynamics with correct rate and correct fluctuation.
>>
>> On Sat, Oct 11, 2014 at 8:09 AM, Dr. Vitaly Chaban 
>> wrote:
>>
>>> what is it needed for?
>>>
>>>
>>>
>>> Dr. Vitaly V. Chaban
>>>
>>> Виталий Витальевич ЧАБАН
>>>
>>>
>>> On Fri, Oct 10, 2014 at 7:41 PM, Johnny Lu 
>>> wrote:
>>> > Hi.
>>> >
>>> > Is it a good idea to mimic NVE by a NVT simulation with a large
>>> temperature
>>> > coupling time constant, to reduce the effect of the thermostat ?
>>> >
>>> > If I use V-rescale thermostat, what artifacts will the simulation get
>>> > if
>>> I
>>> > use a large coupling time (say, 500 ps) and single precision gromacs ?
>>> >
>>> > Thank you.
>>> > --
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>>> posting!
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Re: [gmx-users] Use NVT to mimic NVE

[Dr. Vitaly Chaban]

Well, if it does not conserve total energy, than such a computational
experiment is not reliable. This is a sad truth.

Philosophically, you have two options here. Either you accept that
energy leakage is significant and then you must fight against it
(smaller time-step, double precision, constraints, etc), or -- on the
contrary -- you say that energy loss can be neglected and proceed "as
is".

My personal rule is if the system does not lose more than 2% of total
energy during an entire run, the result is acceptable. I can be
criticized for this voluntary assumption, obviously.

Anyway, tricks with T-coupling constitute a very bad idea in this
case. You basically try to mask the energy leakage problem with the
thermostat. Thermostat never removes the problem itself.


Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН


On Sat, Oct 11, 2014 at 11:12 PM, Johnny Lu  wrote:
> I tried NVE on single precision gromacs 4.6.7 with and without GPU.
> The energy either drift down or up, depending on the mdp file, and the drift
> seems linear.
>
> Linear fit says that if I run 100 ns simulation, at the end the energy is
> doubled.
>
> If I use double precision gromacs, the drift seems insignificant over 100 ns
> simulation by linear regression fitting on a 300 ps run.
> But double precision gromacs can't use gpu and is much slower than single
> precision gromacs.
>
> On Sat, Oct 11, 2014 at 4:33 PM, Dr. Vitaly Chaban 
> wrote:
>>
>> I also cannot get why not to just turn off the thermostat...
>>
>> If energy transfer phenomena are in focus, NVE is an ensemble of
>> choice, no matter which relaxation constant is used for the T-coupling
>> algorithm.
>>
>>
>> Dr. Vitaly V. Chaban
>>
>> Виталий Витальевич ЧАБАН
>>
>>
>> On Sat, Oct 11, 2014 at 6:32 PM, Antonio Baptista 
>> wrote:
>> > Then, run true NVE, for the reasons we already pointed.
>> >
>> > On Sat, 11 Oct 2014, Johnny Lu wrote:
>> >
>> >> For dynamics with correct rate and correct fluctuation.
>> >>
>> >> On Sat, Oct 11, 2014 at 8:09 AM, Dr. Vitaly Chaban 
>> >> wrote:
>> >>
>> >>> what is it needed for?
>> >>>
>> >>>
>> >>>
>> >>> Dr. Vitaly V. Chaban
>> >>>
>> >>> Виталий Витальевич ЧАБАН
>> >>>
>> >>>
>> >>> On Fri, Oct 10, 2014 at 7:41 PM, Johnny Lu 
>> >>> wrote:
>> >>> > Hi.
>> >>> >
>> >>> > Is it a good idea to mimic NVE by a NVT simulation with a large
>> >>> temperature
>> >>> > coupling time constant, to reduce the effect of the thermostat ?
>> >>> >
>> >>> > If I use V-rescale thermostat, what artifacts will the simulation
>> >>> > get
>> >>> > if
>> >>> I
>> >>> > use a large coupling time (say, 500 ps) and single precision gromacs
>> >>> > ?
>> >>> >
>> >>> > Thank you.
>> >>> > --
>> >>> > Gromacs Users mailing list
>> >>> >
>> >>> > * Please search the archive at
>> >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> >>> posting!
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>> >>> > or
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Re: [gmx-users] Lithium Ions in Gromos53A6

[Dr. Vitaly Chaban]

What about taking another alkali ion (are thery any in CROMOS53?) and
adjusting sigma&epsilon to reflect smaller size of Li(+)?

Of course, lithium is a pretty polarizable guy with certain covalent
bonding ambitions, but this does not prevent people to simulate it as
a hard [+1e] sphere...


Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН


On Mon, Oct 6, 2014 at 2:57 PM, Hardy, Adam  wrote:
> Dear All,
>
> I find myself requiring lithium ions in a simulation using (a variant of) the 
> Gromos53A6 forcefield.
>
> Chaging forcefields is not an appealing proposition due to the time already 
> invested in the current one, so I was wondering had any suggestions or has 
> perhaps gone to the effort of creating parameters for it?
>
> Thanks,
>
> Adam Hardy
> PhD Student
> School of Engineering and Physical Sciences
> Heriot-Watt University
> Edinburgh EH14 4AS, UK
>
>
> -
> We invite research leaders and ambitious early career researchers to
> join us in leading and driving research in key inter-disciplinary themes.
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>
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Re: [gmx-users] Use NVT to mimic NVE

[Dr. Vitaly Chaban]

Thus, what is your question now? :-)

The total energy must remain conserved at all times. That's it.


Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН






On Sun, Oct 12, 2014 at 2:45 AM, Johnny Lu  wrote:
> I tried PME and then potential-shift-verlet for Van der Waals. The energy
> is still not constant in mixed precision gromacs 5.0.1 NVE run on 12 xeon
> cpu without gpu. Those were nearly the last few things that I knew that I
> can try in mixed precision. The system has ~165 amino acid, ~9000 water,
> and 3 Cl- ion in a truncated rhombic dodecahedron box. Total energy of the
> following simulation drift constantly down. This production run was a
> continuation of ~300ns npt and ~300ns nvt. The PME grid was 80x80x80.
>
> ; Run parameters
> integrator  = md-vv ; leap-frog integrator
> nsteps  = 15000 ; 1 ns
> dt  = 0.0005; 0.5 fs
>
> ;NVE
> ; nstcomm = 500 ; remove center of mass motion to reduce energy and
> temp. drift. (seems less drift without this)
> shake-tol   = 0.01 ; shake tolerance.
> verlet-buffer-tolerance = 0.0005
>
> ;Output control
> nstenergy   = 20   ; save energies every 1.0 ps
>
> nstlog  = 100   ; update log file every 0.2 ps
> ; Bond parameters
> continuation= yes   ; Restarting after NVT
> constraint_algorithm = lincs; holonomic constraints
> constraints = all-bonds ; all bonds (even heavy atom-H bonds)
> constrained
> lincs_iter  = 2 ; accuracy of LINCS
> lincs_order = 4 ; also related to accuracy
> ; Neighborsearching
> ns_type = grid  ; search neighboring grid cells
> nstlist = 5 ; 10 fs
>
> vdw-modifier = Potential-shift-Verlet;
>
> rlist   = 1.1   ; short-range neighborlist cutoff (in nm)
> rcoulomb= 1.0   ; short-range electrostatic cutoff (in nm)
> rvdw= 1.0   ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype = PME   ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order   = 6 ; cubic interpolation
> fourierspacing  = 0.1   ; grid spacing for FFT
>
> ; Temperature coupling is off
> tcoupl  = no; modified Berendsen thermostat
> ; Pressure coupling is off
> pcoupl  = no
>
> refcoord_scaling = com
> ; Periodic boundary conditions
> pbc = xyz   ; 3-D PBC
> ; Dispersion correction
> DispCorr= EnerPres  ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel = no; Velocity generation is off
> cutoff-scheme = Verlet
>
>
> I guess the energy leakage when no thermostat is used doesn't mean the
> distribution of conformation is incorrect when a thermostat is used.
> Since double precision run is stable while single precision is not, the
> energy leakage is caused by numerical error of the computer operation and
> algorithm instead of the physics or conformation of the setup. (only the
> precision changed. the mdp files were the same.)
>
> I also guess that the majority of simulations in published paper would have
> such constant drop/rise of total energy if the thermostat is switched off.
> ( Is this true??? )
>
> When the Amber99ff-ILDN force field is made, NPT and NVT is used, instead
> of NVE [http://dx.doi.org/10.1002%2Fprot.22711]
>
> The Amber lipid 14 forcefield uses NPT to create the parameters. In one of
> the validations, they ran NPT followed by NVE to calculate diffusion
> coefficient. The tolerance was more stringent in the NVE part than the NPT
> part. The plot of energy v.s. time seems to be not in the paper. [
> http://pubs.acs.org/doi/full/10.1021/ct4010307]
>
> Dynamics is another matter. Langevin thermostats removes momentum transfer
> and changes the rate dynamics, despite it samples the canonical ensemble
> ... if the system is ergodic in practice. Two different simulations can
> converge, if the string of random numbers used in langevin thermostats is
> the same. I'm not sure about V-rescaling.
>
> I agree that all thermostats and barostats likely cause some artifacts in
> dynamics.
>
>
> On Sat, Oct 11, 2014 at 5:29 PM, Dr. Vitaly Chaban 
> wrote:
>
>> Well, if it does not conserve total energy, than such a computational
>> experiment is not reliable. This is a sad truth.
>>
>> Philosophically, you have two options here. Either you accept that
>> energy leakage is significant and then you must fight against it
>> (smaller time-step, double precision, constraints, etc), or -- on the
>> contrary -- you say that energy loss can be neglect

Re: [gmx-users] Acetone parameters and transferability question

[Dr. Vitaly Chaban]

830 versus 791 kg/m^3 is not that terrible discrepancy in the case of
united-atom models and other details from below...

Acetone falls within the group of those small molecules, which are
easy to (re)parameterize.


Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН


On Sun, Oct 12, 2014 at 11:38 AM, Ioanna Styliari
 wrote:
> Hello Justin, and thank you for your reply.
>
> Yes, the diffusion constant with the ATB acetone (code name _LVN) was 
> overestimated in a variety of molar ratios (used SPC water), but also, I am 
> not able to reproduce acetone's experimental density correctly (result was 
> around 830 rather than 791 kg/m^3)
> When building the acetone-solvation boxes, I have followed the guides from 
> Gromacs.
> Another fact is that the second acetone model ATB has, (code name AON, a 
> united atom model for the 53a5ff) is immiscible with water, possibly due to 
> the very low charge in the C=O molecules.
> How can I be certain that the acetone model I use is OK? I am trying to be as 
> careful as possible but really need an expert's advice on which molecule to 
> use.
>
> Again thank you for your time,
>
> Ioanna
>
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Re: [gmx-users] Use NVT to mimic NVE

[Dr. Vitaly Chaban]

The artifacts are caused by energy leakage. Thermostatting does not
solve them. The problem exists, but you do not see it clearly with
thermostat. For instance, I have an example where a liquid droplet in
vacuum is not stable due to bad energy conservation. Some particles
just sporadically fly away over the course of the simulation.

NVE generally does not like constraints. If I remember correctly from
the previous messages, you use constraints. Novel performance
improvements in gromacs (accumulated after 4.0 and especially after
4.5) sometimes compromise accuracy, though it is a long discussion
itself. What about downgrading to gmx 4.0 or gmx 3.3, after all? The
very last time I used gromacs for NVE simulation was in 2009. I guess
I used gmx 3.3.3 (but maybe 4.0.x). There were no problems for sure.

I would also give a try to some very simple system (e.g. liquid argon)
to observe what happens to total energy.

Good luck with troubleshooting!


Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН


On Sun, Oct 12, 2014 at 4:53 PM, Johnny Lu  wrote:
>  Firstly, what are the possible errors/artifacts caused by masking "the
> energy leakage problem with the thermostat" in this case?
>
> Secondly, are there any other mdp setting that I can try to make the mixed
> precision gromacs NVE run have conserved energy over 100 ns ? (and... is it
> because of some errors that I made in my systems that make the NVE run not
> conserved in energy?)
>
> The NVE has the following statistics.
>
> Statistics over 2747281 steps [ 0. through 1373.6400 ps ], 4 data sets
> All statistics are over 274729 points
>
> Energy  Average   Err.Est.   RMSD  Tot-Drift
> ---
> Disper. corr.  -3961.13  0  0 2.60178e-09
> (kJ/mol)
> Total Energy-309939160 337.76478.828
> (kJ/mol)
> Temperature 300.292   0.241.49289   0.631428  (K)
> Pressure   -64.54094.7148.77925.1326  (bar)
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Re: [gmx-users] Use NVT to mimic NVE

[Dr. Vitaly Chaban]

I believe the major problem with energy losses is that your system
never achieves equilibrium.

Thus, all the simulated properties are not what they need to be...




Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН


On Sun, Oct 12, 2014 at 5:31 PM, Dr. Vitaly Chaban  wrote:
> The artifacts are caused by energy leakage. Thermostatting does not
> solve them. The problem exists, but you do not see it clearly with
> thermostat. For instance, I have an example where a liquid droplet in
> vacuum is not stable due to bad energy conservation. Some particles
> just sporadically fly away over the course of the simulation.
>
> NVE generally does not like constraints. If I remember correctly from
> the previous messages, you use constraints. Novel performance
> improvements in gromacs (accumulated after 4.0 and especially after
> 4.5) sometimes compromise accuracy, though it is a long discussion
> itself. What about downgrading to gmx 4.0 or gmx 3.3, after all? The
> very last time I used gromacs for NVE simulation was in 2009. I guess
> I used gmx 3.3.3 (but maybe 4.0.x). There were no problems for sure.
>
> I would also give a try to some very simple system (e.g. liquid argon)
> to observe what happens to total energy.
>
> Good luck with troubleshooting!
>
>
> Dr. Vitaly V. Chaban
>
> Виталий Витальевич ЧАБАН
>
>
> On Sun, Oct 12, 2014 at 4:53 PM, Johnny Lu  wrote:
>>  Firstly, what are the possible errors/artifacts caused by masking "the
>> energy leakage problem with the thermostat" in this case?
>>
>> Secondly, are there any other mdp setting that I can try to make the mixed
>> precision gromacs NVE run have conserved energy over 100 ns ? (and... is it
>> because of some errors that I made in my systems that make the NVE run not
>> conserved in energy?)
>>
>> The NVE has the following statistics.
>>
>> Statistics over 2747281 steps [ 0. through 1373.6400 ps ], 4 data sets
>> All statistics are over 274729 points
>>
>> Energy  Average   Err.Est.   RMSD  Tot-Drift
>> ---
>> Disper. corr.  -3961.13  0  0 2.60178e-09
>> (kJ/mol)
>> Total Energy-309939160 337.76478.828
>> (kJ/mol)
>> Temperature 300.292   0.241.49289   0.631428  (K)
>> Pressure   -64.54094.7148.77925.1326  (bar)
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Re: [gmx-users] Use NVT to mimic NVE

[Dr. Vitaly Chaban]

The point was that if the energy leaves the system, then the system is
never in equilibrium. Not vice versa, please.



Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН


On Sun, Oct 12, 2014 at 7:20 PM, Johnny Lu  wrote:
> Why non-equilibrium can cause lost of total energy in NVE simulation?
> (baring the case that the non-equilibrium causes very large values that
> causes over flow / getting out of the stable range of algorithms of
> gromacs).
>
> A closed system should have constant energy, regardless of whether it is at
> equilibrium.
>
> I guess people use the word "converge" instead of equilibrium in molecular
> dynamics simulation of protein, possibly because the simulation may never
> reach equilibrium with current computing power.
> http://pubs.rsc.org/en/content/articlepdf/2012/cp/c2cp23961b
>
> I may try older version of gromacs and/or not using constraint, after
> checking the bug list and performance. I had never thought about that route.
>
>
>
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Re: [gmx-users] Performance degradation for Verlet cutoff-scheme compared to group

[Dr. Vitaly Chaban]

What about trying a larger system, ~10,000 interaction centers?

The performance which you report is much below natural expectations for GROMACS.



Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН


On Mon, Oct 13, 2014 at 10:55 AM, Олег Титов  wrote:
> Thanks for you reply.
>
> On a different machine I've recompiled GROMACS with icc version 13.1.0 (gcc
> version 4.4.6 compatibility).
> cmake command:
> I_MPI_CC=nvcc CC=icc CXX=icpc cmake ../gromacs-src
> -DCMAKE_INSTALL_PREFIX=~/gromacs-5.0.2/ -DGMX_FFT_LIBRARY=MKL -DGMX_MPI=OFF
> -DGMX_GPU=OFF -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_DEFAULT_SUFFIX=OFF
> -DGMX_BINARY_SUFFIX=_intel -DGMX_LIBS_SUFFIX=_intel
>
> This simulation took 10 hours on 16 CPU cores (15.5 ns/day). Is this normal
> performance for a system with 1641 atoms?
>
> 2014-10-11 1:21 GMT+04:00 Mark Abraham :
>
>> On Fri, Oct 10, 2014 at 8:16 PM, Олег Титов 
>> wrote:
>>
>> > Good day.
>> >
>> > I've got sigmificant performance degradation when trying to use Verlet
>> > cutoff-scheme for free energy calculation. My system contains 1
>> > bromobenzene molecule and 543 TIP3P waters. 16 hours of calculation on
>> > 8-core CPU resulted in 2.5 ns trajectory. With group scheme i've got 6.5
>> ns
>> > trajectory in 7h 40 min.
>> >
>> > Interesting that with group scheme gromacs tells me that it was using 8
>> MPI
>> > threads while with Verlet - 1 MPI and with 8 OpenMP threads. Both times
>> > I've launched the calculation with "mdrun -deffnm test".
>> >
>>
>> One scheme supports OpenMP, one doesn't...
>>
>>
>> > I believe that this is caused by "plain C kernels" as GROMACS warns me.
>> Is
>> > there any possibility to overcome this issue?
>> >
>>
>> Yes...
>>
>>
>> > I have access only to old gcc 4.1.2 (without SSE4.1) and buggy icc 11.1
>> on
>> > this machine.
>> >
>>
>> Gromacs requires a real compiler to get performance, like the install guide
>> says. You need to get one.
>>
>> Mark
>>
>>
>> > Thanks for your help.
>> >
>> > Oleg Titov
>> > --
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Re: [gmx-users] Regarding umbrella samplling

[Dr. Vitaly Chaban]

Yes, it means what you say.

I would decrease the number of bins.



Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН


On Mon, Oct 13, 2014 at 12:47 PM, Johnny Lu  wrote:
> Hi. Does that mean the umbrella don't overlap enough at those z ?
> Can you make an overlay plot of the histograms of each umbrella?
>
> On Mon, Oct 13, 2014 at 1:54 AM, Sathish Kumar 
> wrote:
>
>> Dear gromacs usres,
>>
>>  I have run the umbrella sampling with the help of tutorial of justin. In
>> my system rna is binding with gold nanoparticle. To find out the binding
>> energy, i run the umbrella sampling using the space 0.1 nm and i got total
>> 79 configurations, each configuration was run for 5 ns. Using g_wham, i got
>> the profile.xvg, in that profile.xvg,  all PMF values are zero. while
>> running g_wham i am getting warings like below.
>>
>> WARNING, no data point in bin 163 (z=8.27767) !
>> You may not get a reasonable profile. Check your histograms!
>>
>> WARNING, no data point in bin 164 (z=8.31563) !
>> You may not get a reasonable profile. Check your histograms!
>>
>> WARNING, no data point in bin 165 (z=8.35358) !
>> You may not get a reasonable profile. Check your histograms!
>> Warning, poor sampling bin 194 (z=9.45432). Check your histograms!
>> Initialized rapid wham stuff (contrib tolerance 1.31579e-08)
>> Evaluating only 2619 of 15200 expressions.
>>
>>1) Maximum change 3.178184e+02
>>  100) Maximum change 1.611126e+00
>>  200) Maximum change 3.303540e+00
>>  300) Maximum change 1.239682e+00
>>  400) Maximum change 1.383353e+00
>>  500) Maximum change 1.116406e+00
>>  600) Maximum change 1.241516e+00
>>  700) Maximum change 1.028108e+00
>>  800) Maximum change 1.698508e+00
>>  900) Maximum change 1.331078e+00
>> Switched to exact iteration in iteration 983
>> Converged in 984 iterations. Final maximum change 0
>>
>> Please help me in this regard.
>>
>> Thanks
>> sathish
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Re: [gmx-users] (no subject)

[Dr. Vitaly Chaban]

This usually means that your system is not well equilibrated.



Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН


On Wed, Oct 15, 2014 at 6:13 AM, Padmani Sandhu
 wrote:
> Hello,
>
>
> I am doing Molecular-Dynamic simulation of Protein-Ligand complex embedded
> in POPC lipid membrane. After energy minimizing of complex, I am facing
> problem with NVT equilibration step. mdrun crashed with following error:
>
>
> "12 particles communicated to PME node 4 are more than 2/3 times the
> cut-off out of the domain decomposition cell of their charge group in
> dimension x.
> This usually means that your system is not well equilibrated."
>
>
>
>
> These are the parameters used in nvt.mdp file:
>
> title   = NVT equilibration
>
> define  = -DPOSRES_LIPID -DPOSRES
> -DPOSRES_WATER  ; position restrain the protein
>
> ; Run parameters
>
> integrator  = md; leap-frog integrator
>
> nsteps  = 5 ; 2 * 5 = 100 ps
>
> dt  = 0.002 ; 2 fs
>
> ; Output control
>
> nstxout = 100   ; save coordinates every 0.2 ps
>
> nstvout = 100   ; save velocities every 0.2 ps
>
> nstenergy   = 100   ; save energies every 0.2 ps
>
> nstlog  = 100   ; update log file every 0.2 ps
>
> ; Bond parameters
>
> continuation= 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 cels
>
> 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)
>
> ; Electrostatics
>
> coulombtype = PME   ; Particle Mesh Ewald for
> long-range electrostatics
>
> pme_order   = 4 ; cubic interpolation
>
> fourierspacing  = 0.16  ; grid spacing for FFT
>
> ; Temperature coupling is on
>
> tcoupl  = V-rescale ; modified
> Berendsen thermostat
>
> tc-grps = Protein_LMT POPC Water_and_ions   ;
> three coupling groups - more accurate
>
> tau_t   = 0.1   0.1 0.1 ; time constant, in
> ps
>
> ref_t   = 271   271 271 ; 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= EnerPres  ; account for cut-off vdW
> scheme
>
> ; Velocity generation
>
> gen_vel = yes   ; assign velocities from Maxwell
> distribution
>
> gen_temp= 271   ; temperature for Maxwell
> distribution
>
> gen_seed= -1; generate a random seed
>
> ; COM motion removal
>
> ; These options remove motion of the
> protein/bilayer relative to the solvent/ions
>
> nstcomm = 1
>
> comm-mode   = Linear
>
> comm-grps   = Protein_LMT_POPC Water_and_ions
>
>
>
>
> Please help me...
>
>
>
>
> --
> *Padmani sandhu*
> *Research Scholar,*
> *Center for Computational Biology and Bioinformatics,*
> *Central University of Himachal Pradesh,*
> *Temporary Academic Block, Shahpur *
> *Pin 176206, District Kangra,*
> *Himachal Pradesh, India*
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Re: [gmx-users] 2-D liquid

[Dr. Vitaly Chaban]

I believe 2D liquid is a liquid film. If so, none of your options will work.

You need to surround the liquid film with a layer of vacuum and
simulate NVE ensemble.


Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН


On Wed, Oct 15, 2014 at 6:06 AM, Cai  wrote:
> Hi users,
>
> I am trying to simulate 2-d liquids interacting with simple potential like
> Lennard-Jones potential.
>
> Can it be done by specifying "pcoupletype = semiisotropic" in the .mdp
> file? I mean enforcing a normal pressure in x-y direction while very high
> pressure in z direction to constrain the motion in z.
>
> Or do I need to define walls in the z direction?
>
> Does anyone have similar experience? Your help are highly appreciated!
>
>
> Cai
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Re: [gmx-users] How to add iron parameter?

[Dr. Vitaly Chaban]

"The easiest way" is to simulate QM/MM around Fe (+howmuch?).



Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН


On Wed, Oct 15, 2014 at 7:22 PM, Guangyu Zhu  wrote:
> Hi, I’m a beginner of gromacs. I want to do simulation for a protein with 
> protein with ferrous or ferric. But there is no iron in force field. What is 
> easiest way to do it? Can I just add a few lines to aminocids.rtp, like this?
>
> [FE]
>
>  [ atoms]
>
>FE  FE3.0
>
>  [ bonds]
>
>  [ angles ]
>
>  [ impropers ]
>
>  [ dihedrals ]
>
>
> Thanks!
> Guangyu
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Re: [gmx-users] how to build topology

[Dr. Vitaly Chaban]

I believe only writing the ITP file(s) by hand.


Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН


On Wed, Oct 15, 2014 at 5:49 PM, Victor Rosas Garcia
 wrote:
> Hello everybody,
>
> I want to build a topology for a lipid to use the parameters reported
> by Jämbeck and Lyubartsev
>
> Jämbeck, Joakim P. M., y Alexander P. Lyubartsev. «Derivation and
> Systematic Validation of a Refined All-Atom Force Field for
> Phosphatidylcholine Lipids». J. Phys. Chem. B 116, n.o 10 (2012):
> 3164-79. doi:10.1021/jp212503e.
>
> but the modified forcefield provided by the authors is not included by
> default in Gromacs (I am still using version 4.5.4).
>
> How could I build a topology that uses this modified forcefield?  I
> have tried acpype, but it uses atomtypes different from the ones I
> want.
>
> Best regards
>
> Victor
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Re: [gmx-users] pressure dependence on volume.

[Dr. Vitaly Chaban]

To achieve what you want you need to MANUALLY set the average DENSITY
which you obtained from NPT. That is, you MANUALLY adjust box side
length in the GRO file.



Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН


On Sat, Oct 18, 2014 at 1:47 AM, Johnny Lu  wrote:
> I am trying to transit from NPT to NVT.
> Using the averaged volume of NPT for NVT somehow didn't give me the 1 bar
> pressure in NVT.
> I don't know why that happened.
>
> Was it the difference between constant pressure and constant volume heat
> capacity? But then, the thermostat should take care of that quite quickly.
> After that, N, V, and T would be same for NPT simulation and the NVT
> simulation... which means the pressure should be the same.
>
> Both the NVT and NPT uses the V-rescale thermostat, and the NPT uses
> Berendsen barostat.
>
> Right now I'm selecting NPT frames with different volumes, and see if the
> NVT simulations continuing from those frames would give me the 1 bar
> pressure.
>
> On Fri, Oct 17, 2014 at 3:53 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 10/17/14 11:49 AM, Johnny Lu wrote:
>>
>>> At least for real water, a 0.2% error in volume can mean the pressure is
>>> ~30 bar when the target pressure is 1 bar.
>>> http://docs.engineeringtoolbox.com/documents/309/water-density-
>>> temperature-pressure_2.png
>>>
>>> On Fri, Oct 17, 2014 at 10:49 AM, Johnny Lu 
>>> wrote:
>>>
>>>  Hi.

 Mainly TIP3P water, 300K. The pressure is near 1 bar.

 A less than 1% error in volume would cause how much error in average
 pressure?

  From three npt simulations of 72 ns with Berendsen barostat, I get the
 average volume is 298.5 nm^3.

 Continuing from a frame with volume very close to 298.5 nm^3 (~0.01
 deviation from this volume), I run NVT simulation that at first gives a
 system that doesn't seem to be at equilibrium.


>> Does that time point correspond to the desired pressure?  The pressure
>> tensor is calculated from the virial and the kinetic energy, so those are
>> the quantities you should be looking at for instantaneous pressures.
>>
>> -Justin
>>
>> --
>> ==
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==
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Re: [gmx-users] SWM4-NDP force field

[Dr. Vitaly Chaban]

The assigned masses are due to the presence of dummy atoms. The model
molecule must represent moments of inertia.

1-4 (fudgeLJ and fudgeQQ) interactions do not apply for water. So, you care
about a larger molecule only.


Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН




On Sat, Oct 18, 2014 at 8:39 AM, Kester Wong  wrote:
>
> Dear all,
>
>
>
> I would like to know if this would cause a difference in MD calculations
(text highlighted in red):
>
> The assigned mass for the hydroxide O-atom seems to be inconsistent. Was
the zero atomic mass set with a specific purpose?
>
>
> #define SHELLPTYPE S
>
> #define SHELLMASS  0
>
> #define OXYGENMASS 15.9994
>
>
> [ atomtypes ]
>
> ; name  btype   masscharge   ptype sigmaepsilon
>
>  SWM4-NDP_110a  ODSHELLMASS-1.71636SHELLPTYPE  0.0
   0.0
>
>  SWM4-NDP_OV1   OV1 1.00.0 A   0.24
0.294191
>
>  SWM4-NDP_OV2   OV2 0.00.0 D   0.28
0.294191
>
>  SWM4-NDP_H H   1.008  0.0 A   0.07
0.294191
>
>  SWM4-NDP_qHqH  0.0   0.23 D   0.0  0.0
>
>  SWM4-NDP_O O   0.0  0.203 A   0.0  0.0
>
>
>
> ; Hydroxide
>
> [ moleculetype ]
>
> ; molname   nrexcl
>
> OH-2
>
>
> [ atoms ]
>
> ; idat type res nr  residu name at name  cg nr   charge   mass
>
>  1SWM4-NDP_O   1   OH-   O 1   0.202
 11.998
>
>  2SWM4-NDP_110a1   OH-  OS 1  -1.432
0.00
>
>  3SWM4-NDP_H   1   OH-   H 1   0.00
 1.008
>
>  4SWM4-NDP_OV1 1   OH- OV1 1   0.001.0
>
>  5SWM4-NDP_OV1 1   OH- OV1 1   0.001.0
>
>  6SWM4-NDP_OV1 1   OH- OV1 1   0.001.0
>
>  7SWM4-NDP_OV1 1   OH- OV1 1   0.001.0
>
>  8SWM4-NDP_OV2 1   OH- OV2 1   0.00
 0.00
>
>  9SWM4-NDP_qH  1   OH-  qH 1   0.23
 0.00
>
>
> [ polarization ]
>
> #ifdef POL2WATER
>
> 1 2 2  0.00068090.02   16.736e8
>
> #else
>
> 1 2 1  0.0006809
>
> #endif
>
>
> ; Initialy developed as a harmonic bond
>
> ; Conversion: alpha=sqrt(qS)/(4*pi*eps0*CAL2J*A2NM*k) =  138.9354492 *
sqrt(qS)/k
>
> ; [ bonds ]
>
> ; 1 2 6 0.0 418400
>
>
> [ constraints ]
>
>  3 1 1 0.0968
>
>  4 1 1 0.1463
>
>  5 1 1 0.1463
>
>  6 1 1 0.1463
>
>  7 1 1 0.1463
>
>  4 6 1 0.1979
>
>  6 5 1 0.1979
>
>  5 7 1 0.1979
>
>  7 4 1 0.1979
>
>
> #ifdef CONSTRAINTS
>
> [ constraints ]
>
>  3 4 1 0.15
>
>  3 5 1 0.15
>
>  3 6 1 0.15
>
> ; A fourth constraint would make the system redundant and therefore
>
> ; numerically unstable.
>
> ; 3 7 1 0.15
>
> #else
>
> [ angles ]
>
>  3 1 4 1 73.11 683
>
>  3 1 5 1 73.11 683
>
>  3 1 6 1 73.11 683
>
>  3 1 7 1 73.11 683
>
> #endif
>
>
> [ dummies2 ]
>
> 8 3 1 11.4390
>
> 9 3 1 1   -0.3099
>
>
> [ exclusions ]
>
>  1 2 3 4 5 6 7 8 9
>
>  2 1 3 4 5 6 7 8 9
>
>  3 1 2 4 5 6 7 8 9
>
>  4 1 2 3 5 6 7 8 9
>
>  5 1 2 3 4 6 7 8 9
>
>  6 1 2 3 4 5 7 8 9
>
>  7 1 2 3 4 5 6 8 9
>
>  8 1 2 3 4 5 6 7 9
>
>  9 1 2 3 4 5 6 7 8
>
>
>
> If I am to add/define graphene's bonded and nonbonded parameters into the
SWM4-NDP force field, using CHARMM27 parameters, should I take into
consideration the fudgeLJ and fudgeQQ differences (0.5 fudge LJ and fudgeQQ
in SWM4-NDP, 1.0 for fudgeLJ and fudgeQQ in CHARMM27)? The comb-rules are
the same (no.2).
>
>
>
> Thanks in advance!
>
> Kester
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Re: [gmx-users] pressure dependence on volume.

[Dr. Vitaly Chaban]

I believe you are too concentrated on writing questions, so that it
does not leave you time to think about responses.

Try to learn the manual a bit.

Best luck.

Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН


On Sun, Oct 19, 2014 at 4:18 AM, Johnny Lu  wrote:
> I searched the energy file made by g_energy, and found that NPT frames with
> very similar densities have very similar volume.
>
> So, I guess using density is same as using volume in this case.
>
> On Sat, Oct 18, 2014 at 9:09 AM, Johnny Lu  wrote:
>
>> Would manually setting the box size make vacuum bubbles?
>>
>> On Sat, Oct 18, 2014 at 9:08 AM, Johnny Lu  wrote:
>>
>>> my bad. that formula for density is wrong. But I till don't see why using
>>> the same averaged density (instead of volume) for the NVT and NPT
>>> simulations would give a different result.
>>>
>>> On Sat, Oct 18, 2014 at 8:52 AM, Johnny Lu 
>>> wrote:
>>>
 Was the density calculated by # particles /  volume ?

 If so, using volume (as I did), and using density would give the same
 wrong pressure, upon transitioning from NPT to NVT.

>>>
>>>
>>
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Re: [gmx-users] SWM4-NDP force field

[Dr. Vitaly Chaban]

Hi Kester -

The four dummy atoms carry a mass of 1 a.m.u each, hence the oxygen mass of
11.998.

However, what I don't understand is that the same atom has a mass of 0.0
under [ atomtypes ].

-- The later section overwrites previous one, so it is possible to write
zeros for charges and masses in [atomtypes] if you then write correct
numbers in [atoms]. I believe this situation is due to historical reasons.

For a system consisting of graphene, water and (Na+ OH-, or H3O+ Cl-) ions,
if there is nonbonding-parameters specified, will having a different fudge
value (0.5 instead of 1.0) make a difference?

-- Yes, it will -- but only for graphene. Small particles do not exhibit
1-4 interactions, because they do NOT possess atoms which are separated by
3 covalent bonds, -C-C-C-C-.

1-4 interactions work as a supplement to the dihedral function. To
understand which number (0.5 or 1.0 or what you like) works better, you
will have to compare dihedrals from MD simulations with those you expect
(from X-ray structure, from electronic structure description, etc).
Normally, 1-4 interactions do matter, but they don't make a global
difference.

Best of luck,
Vitaly

Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН




On Mon, Oct 20, 2014 at 6:13 AM, Kester Wong  wrote:

> Hi Dr. Chaban,
>
>
> The four dummy atoms carry a mass of 1 a.m.u each, hence the oxygen mass
> of 11.998.
>
> However, what I don't understand is that the same atom has a mass of 0.0
> under [ atomtypes ].
>
>
> For a system consisting of graphene, water and (Na+ OH-, or H3O+ Cl-)
> ions, if there is nonbonding-parameters specified, will having a different
> fudge value (0.5 instead of 1.0) make a difference?
>
>
> Thank you in advance.
>
>
> Regards,
>
> Kester
> - 원본 메일 -
>
> *보낸사람* : "Dr. Vitaly Chaban" 
> *받는사람* : 
> *받은날짜* : 2014년 10월 18일(토) 16:20:49
> *제목* : Re: [gmx-users] SWM4-NDP force field
>
> The assigned masses are due to the presence of dummy atoms. The model
> molecule must represent moments of inertia.
>
> 1-4 (fudgeLJ and fudgeQQ) interactions do not apply for water. So, you care
> about a larger molecule only.
>
>
> Dr. Vitaly V. Chaban
>
> Виталий Витальевич ЧАБАН
>
>
>
>
> On Sat, Oct 18, 2014 at 8:39 AM, Kester Wong  wrote:
> >
> > Dear all,
> >
> >
> >
> > I would like to know if this would cause a difference in MD calculations
> (text highlighted in red):
> >
> > The assigned mass for the hydroxide O-atom seems to be inconsistent. Was
> the zero atomic mass set with a specific purpose?
> >
> >
> > #define SHELLPTYPE S
> >
> > #define SHELLMASS  0
> >
> > #define OXYGENMASS 15.9994
> >
> >
> > [ atomtypes ]
> >
> > ; name  btype   masscharge   ptype sigmaepsilon
> >
> >  SWM4-NDP_110a  ODSHELLMASS-1.71636SHELLPTYPE  0.0
>0.0
> >
> >  SWM4-NDP_OV1   OV1 1.00.0 A   0.24
> 0.294191
> >
> >  SWM4-NDP_OV2   OV2 0.00.0 D   0.28
> 0.294191
> >
> >  SWM4-NDP_H H   1.008  0.0 A   0.07
> 0.294191
> >
> >  SWM4-NDP_qHqH  0.0   0.23 D   0.0  0.0
> >
> >  *SWM4-NDP_O O   0.0  0.203 A   0.0  0.0*
> >
> >
> >
> > ; Hydroxide
> >
> > [ moleculetype ]
> >
> > ; molname   nrexcl
> >
> > OH-2
> >
> >
> > [ atoms ]
> >
> > ; idat type res nr  residu name at name  cg nr   charge   mass
> >
> >  1*SWM4-NDP_O   1   OH-   O 1   0.202  
> > 11.998*
> >
> >  2SWM4-NDP_110a1   OH-  OS 1  -1.432   0.00
> >
> >  3SWM4-NDP_H   1   OH-   H 1   0.001.008
> >
> >  4SWM4-NDP_OV1 1   OH- OV1 1   0.001.0
> >
> >  5SWM4-NDP_OV1 1   OH- OV1 1   0.001.0
> >
> >  6SWM4-NDP_OV1 1   OH- OV1 1   0.001.0
> >
> >  7SWM4-NDP_OV1 1   OH- OV1 1   0.001.0
> >
> >  8SWM4-NDP_OV2 1   OH- OV2 1   0.000.00
> >
> >  9SWM4-NDP_qH  1   OH-  qH 1   0.230.00
> >
> >
> > [ polarization ]
> >
> > #ifdef POL2WATER
> >
> > 1 2 2  0.00068090.02   16.736e8
> >
> > #else
> >
> > 1 2 1  0.0006809
> >
> >

Re: [gmx-users] OPLSAA

[Dr. Vitaly Chaban]

Yes, it is a typo and not only in this paper.

There is NO plausible explanation why to introduce scaling factors for
the atoms separated by more than 3 bonds.



Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН


On Mon, Oct 20, 2014 at 4:48 AM, Justin Lemkul  wrote:
>
>
> On 10/19/14 1:43 PM, Eric Smoll wrote:
>>
>> Hello Gromacs users,
>>
>> Here is a quote from a JPCB paper with over 500 citations:
>>
>> "In fact, in the specification of the OPLS-AA force field, sites within
>> the
>> same molecule separated by *more than* three bonds interact by
>> Lennard-Jones and electrostatic potentials scaled by a factor of 0.5"
>>
>> Am I correct in assuming that "separated by more than three bonds" is a
>> typo and should "separated by three bonds"? I have read the original OPLS
>> reference (Jorgensen 1996) and it says:
>>
>> "it was found to be necessary to scale the 1,4-nonbonded interaction to
>> permit use of the same parameters for inter- and intramolecular
>> interactions. Scaling factors fij = 1/2 for both the coulombic and
>> Lennard-Jones interactions emerged a  the final choice..."
>>
>> There is no mention of this phrase in the additions and corrections
>> document.
>>
>
> Probably a typo, but that's a question for the authors.
>
>> Gromacs only scales the 1-4 interactions, not all nonbonded interactions
>> beyond three bonds, correct?
>
>
> Yes.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
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Re: [gmx-users] Simulating Multiple Solute Particles

[Dr. Vitaly Chaban]

Hi -

genbox must work. You add the first molecule, then the second molecule
and so on. So, I suggest to run genbox for a few times and have enough
empty space available in the box. Otherwise, there is a wonderful tool
called PACKMOL.

The acid molecule looks pretty sexy. I guess it will not be very
straighforward to capture the effect of the triple bond right near
carboxyl group.


Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН


On Sat, Oct 25, 2014 at 8:23 AM, Nathan K Houtz  wrote:
> Hello, I apologize for any ignorance but I'm quite new to gromacs and am 
> confused about a few things.
>
> I want to run some simulations of a small molecule, tetrolic acid 
> (CH3-C≡C-COOH) dissolved in a box of water. I'm doing this to see if a united 
> atom approximation on the methyl group is sufficiently good for saving a bit 
> of computation time. I have created a .gro file and a .top file and attempted 
> to put it into gromacs but I don't know how to model more than one molecule 
> of TTA. All of the tutorials I've looked up involve solvating enormous 
> proteins and they only do one at a time. I'd like to simulate hundreds of TTA 
> molecules with an appropriate amount of water molecules. I attempted to do 
> this by specifying the numbers of TTA and H2O in my topology file, but when I 
> tried to solvate it, gromacs removed the line specifying how many waters and 
> replaced it with its own number (216) and made the box way too small to fit 
> any more TTA. I feel like this may be trivial, but I'm stuck. I really 
> appreciate anyone's help.
>
> After I figure this out, I'm going to try do dissolve tetrolic acid in 
> chloroform, then ethanol as well. I suspect gromacs doesn't have a built in 
> .gro or .top files for either of those (certainly not chloroform). Would the 
> solvate command work just as well if I created my own?
>
> Thanks in advance!
> N.H.
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[gmx-users] histo-clust.xvg from g_clustsize

[Dr. Vitaly Chaban]

Does anyone happen to remember what the frequencies in
"histo-clust.xvg" from g_clustsize mean?

Are they directly comparable between different systems?


Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН
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Re: [gmx-users] Understanding the results of NVT simulation

[Dr. Vitaly Chaban]

On Wed, Oct 29, 2014 at 6:37 PM, Agnivo Gosai  wrote:
> Dear Users
>
> I did a NVT simulation with the following key parameters :-
>
> ; Temperature coupling
> tcoupl  = V-rescale ; modified Berendsen thermostat
> tc-grps = DNA_Protein Water_and_ions; 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
>
> The g_energy outputs for my nvt.edr file are as follows :-
>
> *For Temperature*
> Last energy frame read 500 time  100.000
>
> Statistics over 50001 steps [ 0. through 100. ps ], 1 data sets
> All statistics are over 10001 points
>
> Energy  Average   Err.Est.   RMSD  Tot-Drift
> --
> -
> Temperature 299.638   0.324.754461.93228  (K)
>
> Question 1 : Is the drift of 1.93 K allowable ??
>
> *For Total Energy*
> Last energy frame read 500 time  100.000
>
> Statistics over 50001 steps [ 0. through 100. ps ], 1 data sets
> All statistics are over 10001 points
>
> Energy  Average   Err.Est.   RMSD  Tot-Drift
> ---
> Total Energy-9216615608454.343197.77
> (kJ/mol)
>
> Question 2 : What is the physical significance of a high Err. Est and a
> high Tot-Drift ? I am unable to understand if my system is behaving

> properly or not.
>
> I use GROMACS 4.5.7 single precision.


According to my taste, everything goes allright. The drift is small
(what's the size of your system?), the error in energy is small (in
pct).

Go forward!

Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН
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Re: [gmx-users] Packmol starting .pdb and proper equilibration

[Dr. Vitaly Chaban]

I do not believe it is because of packmol or because of equilibration.

What about trying a different number of cores per job? Sometimes,
certain number of cores do not want to work correctly for certain
systems.



Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН


On Wed, Oct 29, 2014 at 7:07 PM, Ioanna Styliari
 wrote:
> Dear Gromacs users,
>
> I am simulating a system that contains a drug nanoparticle in amorphous 
> state, surrounded by water and the water is also surrounded by acetone 
> (imagine 2 concentric spheres for the first two inside one big box for the 
> acetone).
>
> I used to build the system using gromacs editconf and more precisely building 
> one box at a time and running em, nvt and npt equilibration for each one of 
> the extra box-layers I was adding. However this was a very tedious procedure 
> so I have started recently building the system using Packmol. Once I get the 
> pdb from packmol I edit it to add the box dimensions with editconf and then 
> go through an em, nvt, npt (usually 100ps) for the whole system.
> I have already run 4-5 simulations of 50ns and 100ns and they were running 
> fine (they are running on parallel in a cluster). However in my last one I 
> got the following error:
>
> Fatal error:
> 1 particles communicated to PME node 20 are more than 2/3 times the cut-off 
> out of the domain decomposition cell of their charge group in dimension y.
>
> I know this means that the system is not well equilibrated but after the nvt 
> and npt the T and P are converged. I have reduced the time step to 1fs but I 
> am also worried that the equilibration is not the correct one. It is also 
> worth saying that I had similar errors even with my previous building 
> procedure using gromacs.
>
> Any suggestions/experiences with using Packmol? I am also attaching my mdp 
> options below just in case.
>
> Thank you very much for your time in advance,
>
> Ioanna Styliari
>
> EM:
> integrator= steep   ; Algorithm (steep = steepest descent 
> minimization)
> emtol = 10.0; Stop minimization when the maximum force < 10.0 
> kJ/mol/nm
> emstep= 0.001   ; Energy step size
> nsteps= 50  ; Maximum number of (minimization) steps to 
> perform
>
> ; Parameters describing how to find the neighbours of each atom and how to 
> calculate the interactions
> Nstlist   = 1   ; Frequency to update the neighbour list and long 
> range forces
> ns_type   = grid; Method to determine neighbour list (simple, 
> grid)
> rlist = 1.0 ; Cut-off for making neighbour list (short range 
> forces)
> coulombtype   = PME ; Treatment of long range electrostatic 
> interactions
> rcoulomb  = 1.0 ; Short-range electrostatic cut-off
> vdw-type  = Cut-off
> rvdw  = 1.0 ; Short-range Van der Waals cut-off
> pbc   = xyz ; Periodic Boundary Conditions
> NVT
> title = pol1-box NVT
> ; Run parameters
> integrator= md  ;
> nsteps= 10  ; 100 ps
> dt= 0.001   ; 1 fs
> ; Bond parameters
> continuation  = no  ; first dynamics run
> ; Neighborsearching
> ns_type   = grid; search neighboring grid cells
> nstlist   = 5   ;
> rlist = 1.0 ; short-range neighborlist cutoff (in nm)
> rcoulomb  = 1.0 ; short-range electrostatic cutoff (in nm)
> rvdw  = 1.0 ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype   = PME ; Particle Mesh Ewald for long-range 
> electrostatics
> pme_order = 4   ; cubic interpolation
> fourierspacing   = 0.16; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl= V-rescale   ; modified Berendsen thermostat
> tc-grps   = system  ;
> tau_t = 0.1 ; time constant, in ps
> ref_t = 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  = EnerPres; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel   = yes ; assign velocities from Maxwell distribution
> gen_temp  = 300 ; temperature for Maxwell distribution
> gen_seed  = -1  ; generate a random seed
>
> constraints   = none
>
> NPT
> title = pol1-box NPT
> ; Run parameters
> integrator= md
> nsteps= 10
> dt= 0.001
> ; Bond parameters
> continuation  = yes ; Restarting after NVT
> ; Neighborsearching
> ns_type   = grid; search neighbouring grid cells
> nstlist   = 5   ;  fs
> rlist = 1.0 ; short-range neighbourlist cutoff (in nm)
> rcoulomb  = 1.0 ; short-range electrostatic cutoff (in nm)
> rvdw  = 1.0 ; short-range van der Waa

Re: [gmx-users] Pressure coupling and liquid crystals

[Dr. Vitaly Chaban]

The only reason to use semi-isotropic or anisotropic pressure coupling
is your own desire to control pressure components, XX ... ZZ,
differently.

In the case of liquid crystals, I would use semi-isotropic coupling,
but rather perceiving this as a matter of my own taste.


Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН


On Wed, Oct 29, 2014 at 12:27 PM, Todor Antonijevic  wrote:
> Hi,
>
> I know that in the case of bilayer membranes people use semi-isotropic
> pressure coupling, but what about simulating liquid crystals other then
> bilayer membranes, say three layers of liquid crystal molecules? Should I
> use semi-isotropic pressure coupling? Is there any tutorial on this subject?
>
> Thanks.
>
> P.S: Where can I find Gromacs Workshop 2007?
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Re: [gmx-users] Long bond streches during simulations

[Dr. Vitaly Chaban]

It is disgusting that the bond dares to stretch... Perhaps, there is
no harmonic bond record for this bond in the topology?

Would you like to provide numbers characterizing this long stretch, perhaps?


Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН


On Wed, Oct 29, 2014 at 11:21 AM, Seera Suryanarayana
 wrote:
> Dear gromacs users
>
> I have done mdrun upto 50ns by using the command "gmx mdrun -deffnm md_0_1
> -nt 7.
> I have total 8 threads  and I used 7 out of it along with graphic card
> nvidia tesla 2075.
>
> I first thing I would like to know that when I load the .trr or .xtc file
> after the .gro file into the vmd  some bonds stretched very long are being
> appeared parallel and vertical in red and white color. My question here is
> "Appearing  long bond stretches  while loading into vmd right or wrong?"
>
> At the end of the simulation my protein moves towards the side of the box.
> After some time (frame no. 1564)  few residues moves away from protein and
> some bonds stretched very long being appeared between that residues and
> rest of protein.
>
> Then the bond stretches  disappear from the frame number 1900 and again the
> bond stretch  being appeared during  rest of the simulation and at the end
> I got the final trajectory with some long bond stretching between some
> residues those moved away from the protein and the rest of the protein.
>
> Kindly inform me what could be the reason for the long bond stretching?
>
> Thanks in advance
> Surya
> Graduate student
> India
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Re: [gmx-users] Silica monolayer with Martini force field

[Dr. Vitaly Chaban]

Honestly, I did not get why fixed alkane molecules should interact
with water in a different manner than "normal" ones...


Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН



>
> On Tue, Oct 28, 2014 at 5:22 PM, RAMON REIGADA SANZ  wrote:
>
>> Hi Gromacs users,
>>
>>I want to simulate a monolayer of alkane molecules attached to a solid
>> glass surface. I wonder if anyone has experience with these kinds of
>> systems with the Martini force field. My idea is to add water to the
>> surface and I am interested in what happens between water and the fixed
>> alkanes, so I will freeze the solid beads and the first carbon of the
>> alkane chain.
>> My question is what kind of beads would correspond to glass (silica)
>> surface? Somewhere I found that 'Na' beads could be used to simulate a Pt
>> surface, but I do not know if this would work in my case.
>> Did anyone has experience simulating solid surfaces with Martini?
>>
>>   thank you,
>>
>>   Ramon
>>
>>
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>
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>
> Prof. Dr. André Farias de Moura
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Re: [gmx-users] Regarding the Pi-Pi and pi-cation interaction

[Dr. Vitaly Chaban]

On Thu, Oct 30, 2014 at 5:55 AM, rama david  wrote:
> Dear Friends,
>
>  I search the archive to find the answer of my question but I did not get
> satisfied answer so I am putting the question in forum.
>
> One of them is as
> http://comments.gmane.org/gmane.science.biology.gromacs.user/51771
>
> I want to study the MD simulation of Ligand and Receptor that is stabilize
> by
>  Pi-Pi and pi-cation interaction
>
> 1.  Is it right to say the  Pi-Pi and pi-cation interaction can be studied
> by Moleculardynamics??


No doubts, they can be studied using pairwise interaction potentials within MD.


> 2.  Which force field I have to use ??


I believe all biological FFs maintain pi-pi through adjusted LJ terms.
The difference, as always, is in accuracy, and accuracy in the case of
simulations is a matter of your luck.


> 3. In the analysis tools I found that no direct tools can do this directly.
> How to do this analysis


In terms of energetics.


Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН









> I am looking forward for reply.
>
> With best regards,
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Re: [gmx-users] NPT Simulation average pressure lower than Reference set pressure

[Dr. Vitaly Chaban]

Sampling over 100 ps is incredibly meaningful...


Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН


On Thu, Oct 30, 2014 at 6:49 AM, Agnivo Gosai  wrote:
> Dear Users
>
> I have a DNA-Protein system and I use AMBER99SB-Parmbsc0 ff in GROMACS
> 4.5.7 single precision.
>
> My earlier work flow
> 1) Topology preparation
> 2) Box , Solvation and Ions
> 3) Energy minimization - Steepest descent
> 4) NVT equilibration using a V-rescale thermostat and ref temp = 300 K
>  average temp = 299.7 K after 100 ps NVT sim.
> 5) Next is NPT sim ( with same thermostat on )
>
> *Pressure Coupling part of npt.mdp file :*
>
> ; Pressure coupling is on
> pcoupl  = Berendsen ; Pressure coupling on in NPT, also
> weak coupling
> pcoupltype  = isotropic ; uniform scaling of x-y-z box vectors
> tau_p   = 2.0   ; time constant, in ps
> ref_p   = 1.0   ; reference pressure (in bar)
> compressibility = 4.5e-5; isothermal compressibility, bar^-1
> refcoord_scaling= com
>
>
> *Content of npt.log file :*
>
> Last step --- >
>
>  Energies (kJ/mol)
>   AngleProper Dih.  Improper Dih.  LJ-14 Coulomb-14
> 1.05446e+041.32866e+046.07202e+025.40636e+034.12184e+04
> LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
> 1.46731e+05   -1.93498e+03   -1.23170e+06   -1.17442e+051.30130e+03
>   PotentialKinetic En.   Total EnergyTemperature Pres. DC (bar)
>-1.13198e+062.06576e+05   -9.25405e+052.99973e+02   -7.72790e+01
>  Pressure (bar)   Constr. rmsd
>-5.57060e+000.0e+00
>
> *g_energy output of npt.edr :*
>
> A)Statistics over 50001 steps [ 0. through 100. ps ], 1 data sets
> All statistics are over 10001 points
>
> Energy  Average   Err.Est.   RMSD  Tot-Drift
> --
> -
> Pressure-5.57066.284.808538.1219  (bar)
>
> (B)All statistics are over 10001 points
>
> Energy  Average   Err.Est.   RMSD  Tot-Drift
> --
> -
> Density 1012.13   0.551.871723.17412
> (kg/m^3)
>
>
> *My run parameters are :*
> ; Run parameters
> integrator  = md; leap-frog integrator
> nsteps  = 5 ; 2 * 5 = 100 ps
> dt  = 0.002 ; 2 fs
>
> My reference pressure is 1 bar , the average pressure is -5.5 bar . I
> believe that the system failed to achieve the reference set pressure.
>
>
> *So should I carry out the simulation for a longer time ?? Or should I use
> a different barostat on the next NPT run or do it in a fresh NPT run.*
>
> *Kindly suggest.*
>
>
> Thanks & Regards
> Agnivo Gosai
> Grad Student, Iowa State University.
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Re: [gmx-users] Packmol starting .pdb and proper equilibration

[Dr. Vitaly Chaban]

On Thu, Oct 30, 2014 at 12:30 PM, Ioanna Styliari
 wrote:
> Thank you both for your prompt replies.
>
> Dr Vitaly Chaban: Is there any way of evaluating how many nodes are needed or 
> is it just by a trial-error approach?


If your number of cores gives an error, try another number of cores.


Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН




> Justin: Although 1fs works, I was aiming for 2fs steps in the MD but it 
> crashes. I was thinking to run the first 2ns with 1fs and then try to 
> continue it with 2fs onwards to see what happens, but it crashed at 700ps of 
> my MD. I am using GROMOS96 53a6.
> My equilibration "concern" regards the system: should it be equilibrated as a 
> whole or should I equilibrate one part of it at a time, keeping the others 
> fixed? (which was a suggestion I had but I am unsure how to do it)
>
> Again, thank you
>
> Ioanna
>
> _ _ _ _ _ _ _ _ _ _ _ _ _
> Miss Ioanna Danai Styliari
> PhD Candidate
> Centre for Doctoral Training in
> Targeted Therapeutics and Formulation Sciences
> School of Pharmacy
> University of Nottingham
> Nottingham
> NG7 2RD
> Email: pax...@nottingham.ac.uk
> Telephone: 0044 (0) 74 49890176
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Re: [gmx-users] size of the box for peptide

[Dr. Vitaly Chaban]

the layer of water must be thicker than the interaction cut-off.




Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН


On Mon, Nov 3, 2014 at 8:44 PM, leila salimi  wrote:
> Dear gromacs users,
>
> I want to simulate the conformation of peptide in solution (20 monomers of
> Glutamate with solution). I am in doubt about the size of the box, and
> number of water molecules.
> I want to consider rhombic dodecahedron box. For example I chose a box with
> approximately 498 nm^3 that contain 16369 water molecules.
> I did NVT and NPT equilbiration and I checked the density and it is fine.
> My question is that how I can chose the smallest cell that also no
> interaction between peptides form neighbouring PBC cell.
>
> As I want to use BP-REMD simulations, it is important to have the efficient
> size of the system without any interaction between polymers.
>
> Thanks very much,
> Leila
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Re: [gmx-users] Simulating Carbon nanotubes as finite systems in GROMACS

[Dr. Vitaly Chaban]

I believe once you have a topology (bonds...), it is easy to adapt it to
any external force field...

x2top generates topologies for nanotubes.

genbox adds water.

Other things can be done by hand.



On Fri, Dec 5, 2014 at 1:47 PM, Sergio Manzetti  wrote:

> Dear all, is there a procedure with respective conversion software to run
> a combination of carbon nanotubes (~10å long) with water in GROMACS with
> the GAFF force field?
>
> Currently, PRODRG, ACpype, MKTOP and OBGMX all fail to make a topology of
> CNTs compatible with GAFF force field.
>
> Thanks,
>
> Sergio
>
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[gmx-users] segfault in g_clustsize

[Dr. Vitaly Chaban]

What can segmentation fault in g_clustsize indicate?

The error occurs irrespective of which atom type for clustering we select.
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Re: [gmx-users] segfault in g_clustsize

[Dr. Vitaly Chaban]

UPD: all other utilities process this trajectory without problems
generating adequate numerical results.



On Tue, Jan 20, 2015 at 5:11 PM, Dr. Vitaly Chaban 
wrote:

> What can segmentation fault in g_clustsize indicate?
>
> The error occurs irrespective of which atom type for clustering we select.
>
>
>
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Re: [gmx-users] segfault in g_clustsize

[Dr. Vitaly Chaban]

Mark - I could have said this myself... It reports segfault when the system
contains just a single cluster, but in that case the output files are
created and contain numerical data. In my current case, the files are
created but do not contain anything. - Vitaly



On Tue, Jan 20, 2015 at 5:58 PM, Mark Abraham 
wrote:

>
>
> On Tue, Jan 20, 2015 at 8:11 PM, Dr. Vitaly Chaban 
> wrote:
>
>> What can segmentation fault in g_clustsize indicate?
>>
>
> Usage error, coding error, or insufficient resources. Hard to say which,
> on the information you've given ;-)
>
> Mark
>
>
>> The error occurs irrespective of which atom type for clustering we select.
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Re: [gmx-users] Free energy calculation of a charged system

[Dr. Vitaly Chaban]

Hi Valentina -

Honestly, I did not get the considerations with charges. TI probably
scales interaction energies between selected groups, not charges.

Science-wise, I would first decouple organic particle, then decouple
chloride anions,  and place a right sign between these two free
energies. If you substitute an ion in the neutral system by a
molecule, your system free energy will not definitely like this giving
a positive (delta)G.


Dr. Vitaly V. Chaban


On Fri, Mar 14, 2014 at 4:52 PM, Valentina
 wrote:
> Hello,
>
> I need an advise on how it is better to approach the ThermoD integration of
> such system:
> +vely charged inorganic layer, filled with water and counterbalanced by -ve
> organics
>
> Do I integrate out organics both VdW and Coulomb, making the system have
> total +ve charge at lambda = 1
>
> OR:
>
> Do I integrate out organics only by VdW, leaving Couloumb interactions, by
> such having a neutral system at lambda = 1
>
> I ideally want to compare the free energies of the substituting Cl- ions
> with organic molecules, but I don't think I can just change Cl- at lambda =0
> for an organics at lambda =1 (or can I?) Therefore I was planning to perform
> Thermod integration of both systems independently, also Cl- and organics in
> vacuum (again charges issue) and calculate partition ratios.
>
> Thank you for advise,
> V
>
> --
> View this message in context: 
> http://gromacs.5086.x6.nabble.com/Free-energy-calculation-of-a-charged-system-tp5015154.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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Re: [gmx-users] Function type Fourier Dih. not implemented in ip_pert

[Dr. Vitaly Chaban]

Since I do not couple intramolecular interactions, why those dihedrals
play any role?

Thank you.

Dr. Vitaly V. Chaban


On Mon, Mar 31, 2014 at 5:33 PM, Dr. Vitaly Chaban  wrote:
> Program mdrun_mpi, VERSION 4.6.2
> Source code file:
> /gromacs-2014.01.14-12-21-22-nbreLi.itsi/gromacs-4.6.2/src/gmxlib/topsort.c,
> line: 136
>
> Fatal error:
> Function type Fourier Dih. not implemented in ip_pert
>
> What is this while running free energy code? How to get rid og it?
>
>
> free-energy = yes
> nstdhdl = 10
> couple-moltype = to
> sc-power = 1
> sc-sigma = 0.3
> sc-alpha = 1.0
> couple-intramol = no
> couple-lambda1 = vdw-q
> couple-lambda0 = none
> foreign-lambda = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0
> init-lambda = 0.1
>
>
> Dr. Vitaly V. Chaban
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[gmx-users] Function type Fourier Dih. not implemented in ip_pert

[Dr. Vitaly Chaban]

Program mdrun_mpi, VERSION 4.6.2
Source code file:
/gromacs-2014.01.14-12-21-22-nbreLi.itsi/gromacs-4.6.2/src/gmxlib/topsort.c,
line: 136

Fatal error:
Function type Fourier Dih. not implemented in ip_pert

What is this while running free energy code? How to get rid og it?


free-energy = yes
nstdhdl = 10
couple-moltype = to
sc-power = 1
sc-sigma = 0.3
sc-alpha = 1.0
couple-intramol = no
couple-lambda1 = vdw-q
couple-lambda0 = none
foreign-lambda = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0
init-lambda = 0.1


Dr. Vitaly V. Chaban
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Re: [gmx-users] Function type Fourier Dih. not implemented in ip_pert

[Dr. Vitaly Chaban]

Exactly. So is there any chance to circumvent the problem?


Function type Fourier Dih. not implemented in ip_pert


Dr. Vitaly V. Chaban


On Mon, Mar 31, 2014 at 5:49 PM, Justin Lemkul  wrote:
>
>
> On 3/31/14, 11:35 AM, Dr. Vitaly Chaban wrote:
>>
>> Since I do not couple intramolecular interactions, why those dihedrals
>> play any role?
>>
>
> The couple-intramol option only applies to intramolecular nonbonded
> interactions.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA 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
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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Re: [gmx-users] MD simulations on a remote workstation

[Dr. Vitaly Chaban]

I believe the answer pretty much depends on how large speedup you get
with your present setup. Would you provide this info?



Dr. Vitaly V. Chaban


On Wed, Apr 2, 2014 at 7:14 PM, Amjad Farooq  wrote:
> Hi everyone,
>
> I am running Gromacs 5.0-beta on a remote workstation (next door) from my
> PC. The two machines are networked via 1-Gigabit PCI-E ethernet cards (on
> each machine) and a CAT-6 ethernet cable.
>
> My question is:
> Would my MD simulations benefit in terms of speed if I were to use
> 10-Gigabit PCI-E ethernet cards (they are damn expensive)? Is it worth my
> dime and time? How much would I gain in terms of speed? Halve the run time?
> Or even better?
>
> Thank you for any suggestions that you may have.
>
> Amjad Farooq
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Re: [gmx-users] drug-drug interaction energy

[Dr. Vitaly Chaban]

The positive values must be expected only if the drugs are ionized...



Dr. Vitaly V. Chaban


On Wed, Apr 2, 2014 at 6:23 PM, Manuel Azenha  wrote:
> Dear all,
>
>
>
> When I simulate a solution of a drug in water/methanol to study the
> self-aggregation, and try to determine the interaction energy between the
> drug molecules , I'm getting net positive values whatever the drug. I'm
> simply defining the drug groups in .mdp. Should it be entered some other way
> ?
>
>
>
> Thanks,
>
> Manel
>
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Re: [gmx-users] MD simulations on a remote workstation

[Dr. Vitaly Chaban]

If you want a simple response, then it is NO.



Dr. Vitaly V. Chaban


On Wed, Apr 2, 2014 at 9:35 PM, Amjad Farooq  wrote:
> I have nothing to compare to! Well, I could run the same simulaton directly
> on the workstation itself. May be I should do that. But, realistically, I
> will have to run the test simulation for at least a month (with everything
> else being equal) to get any meaningful comparison.
>
> Anyway, I am wondering whether it would be worth the effort to upgrade my
> 1-Gb ethernet card to 10-Gb? If I am gonna get a mere 10% improvement in
> speed then that is rubbish. But, if that is gonna translate into 100%
> improvement (halve the production run time), then it is worth upgrading.
>
> That remains to be seen.
>
> Amjad
>
>
>
> On Wed, Apr 2, 2014 at 2:44 PM, Dr. Vitaly Chaban 
> wrote:
>>
>> I believe the answer pretty much depends on how large speedup you get
>> with your present setup. Would you provide this info?
>>
>>
>>
>> Dr. Vitaly V. Chaban
>>
>>
>> On Wed, Apr 2, 2014 at 7:14 PM, Amjad Farooq  wrote:
>> > Hi everyone,
>> >
>> > I am running Gromacs 5.0-beta on a remote workstation (next door) from
>> > my
>> > PC. The two machines are networked via 1-Gigabit PCI-E ethernet cards
>> > (on
>> > each machine) and a CAT-6 ethernet cable.
>> >
>> > My question is:
>> > Would my MD simulations benefit in terms of speed if I were to use
>> > 10-Gigabit PCI-E ethernet cards (they are damn expensive)? Is it worth
>> > my
>> > dime and time? How much would I gain in terms of speed? Halve the run
>> > time?
>> > Or even better?
>> >
>> > Thank you for any suggestions that you may have.
>> >
>> > Amjad Farooq
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>> >
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>> > send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] extended bonds

[Dr. Vitaly Chaban]

So, "between" or "intra"?

"extended intramolecular bonds between cosolvent molecules"
Dr. Vitaly V. Chaban


On Wed, Apr 2, 2014 at 8:31 PM, pratibha  wrote:
> Hi all
>
> I have done simulations of my protein in water-cosolvent system (random
> initial addition) at 450K. At the end I have used:
> trjconv -f *.xtc -s *.tpr -center -pbc whole -o new.xtc
> But when I view my trajectory in vmd, I can see extended intramolecular
> bonds between cosolvent molecules. This problem usually come when pbc is not
> taken care off. But in my case I have used trjconv (as above) to account
> this. Is there something wrong in my simulations? I have never encountered
> such problem before at lower temperature of 300K.
> If needed I can attach my *.mdp file.
>
> Thanks in advance.
>
> --
> View this message in context: 
> http://gromacs.5086.x6.nabble.com/extended-bonds-tp5015582.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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Re: [gmx-users] The sum of the two largest charge group radii is larger than rlist

[Dr. Vitaly Chaban]

do you have your protein as a single charge group?



Dr. Vitaly V. Chaban


On Mon, Apr 7, 2014 at 11:48 AM, pratibha  wrote:
> Hi all
>
> I would like to first quench my system from 500K to 300K and then do NPT
> eqilibration followed by NPT production run. But while running grompp for
> NPT eqilibration, I am getting following error :
>
>   The sum of the two largest charge group radii (10.876598) is larger than
> rlist (1.00)
>
>  My system contains protein, cosolvent and water molecules. I think my mdp
> settings are incompatible with the algorithm.
> I am using following parameters for quenching :
>
> ; Run parameters
> integrator  = md; leap-frog integrator
> nsteps  = 10; 0.002 * 10 = 200 ps
> dt  = 0.002 ; 2 fs
> ; Output control
> cutoff-scheme   = Verlet
> nstxout = 1000  ; save coordinates every 2 ps
> nstvout = 1000  ; save velocities every 2 ps
> nstxtcout   = 1000  ; xtc compressed trajectory output every 2
> ps
> nstenergy   = 1000  ; save energies every 2 ps
> nstlog  = 1000  ; update log file every 2 ps
> ; Bond parameters
> ;continuation   = yes   ; Restarting after NPT
> constraint_algorithm = lincs; holonomic constraints
> constraints = all-bonds ; all bonds (even heavy atom-H bonds)
> constrained
> lincs_iter  = 1 ; accuracy of LINCS
> lincs_order = 4 ; also related to accuracy
> ; Neighborsearching
> ns_type = grid  ; search neighboring grid cells
> nstlist = 5 ; 10 fs
> rlist   = 1.0   ; short-range neighborlist cutoff (in nm)
> rcoulomb= 1.0   ; short-range electrostatic cutoff (in nm)
> rvdw= 1.0   ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype = PME   ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order   = 4 ; cubic interpolation
> fourierspacing  = 0.16  ; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl  = V-rescale ; modified Berendsen thermostat
> tc-grps = Protein Non-Protein   ; 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 on
> pcoupl  = Parrinello-Rahman ; Pressure coupling on in NPT
> pcoupltype  = isotropic ; uniform scaling of box vectors
> tau_p   = 2.0   ; time constant, in ps
> ref_p   = 1.0   ; reference pressure, in bar
> compressibility = 4.5e-5; isothermal compressibility of water,
> bar^-1
> ; Periodic boundary conditions
> pbc = xyz   ; 3-D PBC
> ; Dispersion correction
> DispCorr= EnerPres  ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel = no; Velocity generation is off
> ; Quenching
> annealing = single single
> annealing_npoints = 21 21
> annealing_time = 0 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160
> 170 180 190 200 0 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170
> 180 190 200
> annealing_temp = 500 490 480 470 460 450 440 430 420 410 400 390 380 370 360
> 350 340 330 320 310 300 500 490 480 470 460 450 440 430 420 410 400 390 380
> 370 360 350 340 330 320 310 300
>
> And for NPT equilibration I am using :
>
> define  = -DPOSRES  ; position restrain the protein
> ; Run parameters
> integrator  = md; leap-frog integrator
> nsteps  = 5 ; 2 * 5 = 100 ps
> dt  = 0.002 ; 2 fs
> ; Output control
> nstxout = 100   ; save coordinates every 0.2 ps
> nstvout = 100   ; save velocities every 0.2 ps
> nstenergy   = 100   ; save energies every 0.2 ps
> nstlog  = 100   ; update log file every 0.2 ps
> ; Bond parameters
> continuation= yes   ; Restarting after NVT
> constraint_algorithm = lincs; holonomic constraints
> constraints = all-bonds ; all bonds (even heavy atom-H bonds)
> constrained
> lincs_iter  = 1 ; accuracy of LINCS
> lincs_order = 4 ; also related to accuracy
> ; Neighborsearching
> ns_type = grid  ; search neighboring grid cells
> nstlist = 5 ; 10 fs
> rlist   = 1.0   ; short-range neighborlist cutoff (in nm)
> rcoulomb= 1.0   ; short-range electrostatic cutoff (in nm)
> rvdw= 1.0   ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype = PME   ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order   = 4 ; cubic interpolation
> fourierspacing  = 0.16  ; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl  = V-re

[gmx-users] make_ndx, boolean operations

[Dr. Vitaly Chaban]

Hi Everyone -

What is my command line if I need to exclude sites belonging to group
#2 from group #1?

Thank you.


Dr. Vitaly V. Chaban
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Re: [gmx-users] make_ndx, boolean operations

[Dr. Vitaly Chaban]

seems I achieved that with

1 & ! 2



Dr. Vitaly V. Chaban


On Mon, Apr 14, 2014 at 1:52 PM, Dr. Vitaly Chaban  wrote:
> Hi Everyone -
>
> What is my command line if I need to exclude sites belonging to group
> #2 from group #1?
>
> Thank you.
>
>
> Dr. Vitaly V. Chaban
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Re: [gmx-users] Aromatic rings not plane after minimization

[Dr. Vitaly Chaban]

On Tue, Apr 15, 2014 at 10:39 AM, Pierre THEVENET  wrote:
> Hello everyone,
>
> I am using gromacs to perform a small minimization of the structure of my
> peptides, and some have aromatics rings (in tyrosines for example) . Before
> the minimization the ring is perfectly plane (CB-CG and CZ-OH bonds are in
> the same plane than the aromatic ring). However, after the minimization,
> the angle is different and I don't understand why. I tried different
> gromacs versions (
> 4.6.3 and 3.3.3), also different force fields included with gromacs, and I
> always have the loss of the perfect plane angle.
>
> The atom typing is correct, I tried to see if options in my mdp file could
> be the cause of this issue but I couldn't find any option that could be
> responsible for such trouble.
>
> Can someone help me?


Aromatic rings are literally delighted to deform, unless improper
dihedrals are defined in the topology.

I do not know how you do the magic connected with the topology
derivation, but please make sure that all needed dihedrals were
introduced. x2top, for instance, does not write dihedrals.

It is very unlikely that the MDP options can play any role in this problem.



Dr. Vitaly V. Chaban



> Thank you.
>
> --
>
> Pierre THEVENET
> Ph.D. Student
> INSERM - MTi
> Ecole Doctorale B3MI
> Université Paris Diderot - Paris 7
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Re: [gmx-users] Potential for Frozen atoms

[Dr. Vitaly Chaban]

Hi Sukriti Gupta -

Your setup is great. The only scientific problem is that all those
divalent cations in the force fields are being parametrized, to a
larger or a smaller extent, with condensed systems in mind. That is,
if you use them in the liquid phase and for temperature-driven
dynamics, the performance is trustworthy. If without solvent, I would
better employ a bit of QM.

Also, I do not see much difference between using two Cu(++) ions at a
given distance and using two +2e charges at the same distance. Thus,
E=(4*q*q/r)*prefactor.


Dr. Vitaly V. Chaban


On Wed, Apr 16, 2014 at 6:07 AM, sukriti002  wrote:
> Hi,
>
> I wanted to find out site-site potential between two Copper(Cu+2) ions at a
> particular distance and fixed geometry. So I constructed a box containing 2
> Cu+2 and 2 sulfate ions very far away to make the system charge zero. Then i
> froze these atoms and did energy minimization step. But in result I get zero
> potential energy. Can anyone please let me know what went wrong? I can i
> find out this potential at a particular ion-ion distance?
>
> Thanks and Regards
> Sukriti Gupta
>
> --
> View this message in context: 
> http://gromacs.5086.x6.nabble.com/Potential-for-Frozen-atoms-tp5015870.html
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Re: [gmx-users] Is viscosity increasing in the system due to the protein unfolding?

[Dr. Vitaly Chaban]

First, it is unlikely that 'g_energy -f x.edr -o visc.xvg' provides
you a viscosity.

Second, viscosity from equilibrium MD should converge vs. time before
it can be analyzed. I guess what you observe is viscosity convergence,
not viscosity evolution in response to unfolding.


Dr. Vitaly V. Chaban


On Tue, Apr 29, 2014 at 12:30 PM, fatemeh ramezani  wrote:
> Dear Gromacs users
>
> I performed a simulation about the protein adsorption on the gold surface. 
> Protein fluctuation increased and it  denatured after 10 ns simulation. By 
> calculating the viscosity of system by g_energy -f x.edr -o visc.xvg, I 
> founded that viscosity is increasing during the simulation. Due to the fact 
> that by unfolding of protein its viscosity increase, can I relate the 
> viscosity arising to the unfolding of protein?
>
> Fatemeh Ramezani
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Re: [gmx-users] MD simulation at pH 2

[Dr. Vitaly Chaban]

Nice to know that acidic pH simulations are that easy.

Why do you conclude that you achieved pH 2?

Dr. Vitaly V. Chaban


On Fri, May 9, 2014 at 3:45 PM, Turgay Cakmak  wrote:
> Hi all,
>
>
> I have the 8-residue peptide and I want to do Molecular Dynamics
> simulations at pH 2 (with explicit solvent).
>
>
> To do this, I added three Hydrogen atoms to two of the 8-residue peptite
> (one Hydrogen to the Glu, two Hydrojen to the Asp). And also I choose the
> NH3 for the start terminus and COOH for the end terminus. Finally, I get
> the my peptide at pH 2. And than, I plan to follow the usual procedure
> (define box, fill the box with water, energy minim, md...)
>
>
> But, still I am not sure whether this way is correct to get simulation at
> pH 2 or not? Because when I look at the XXX.gro file (and also topol.top)
> after the pdb2gmx –f XXX.pdb, I couldn’t see the new-added hydrogens.
>
>
>
> If you could help me, I would be very happy.
>
>
> with my best regards,
>
> Turgay
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Re: [gmx-users] Generating Glycerol parameters from propanol parameters - OPLS

[Dr. Vitaly Chaban]

I would better start from lipids containing GLY backbone then from propanol...

In any case, basic tests, such as vaporization energy & density
comparison, will be required.

Good luck.

Dr. Vitaly V. Chaban


On Sun, May 25, 2014 at 6:28 PM, Carlos Navarrro Retamal
 wrote:
>
> Dear gromacs users,
> I’m trying to generate the parameters of Glycerol to use them on OPLS.
> I was looking them everywhere without luck, but then i realised that on the 
> folder of OPLS on gromacs are the parameters of propanol.
> So i was wondering, it is ok if i just changed the atoms (at its respective 
> charge) in order to use this parameters in my simulations?
> Is there anything else i should also changed on the .itp file?
> Hope someone can help me,
> Have a nice day.
> Greetings,
> --
> Carlos Navarro Retamal
> Bioinformatic engineer
> PhD student in Applied Science, Universidad de Talca, Chile
> Center of Bioinformatics and Molecular Simulations (CBSM)
> Universidad de Talca
> 2 Norte 685, Casilla 721, Talca - Chile
> Teléfono: 56-71-201 798,
> Fax: 56-71-201 561
> Email: carlos.navarr...@gmail.com or cnava...@utalca.cl
>
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Re: [gmx-users] CNT ROTATION

[Dr. Vitaly Chaban]

This sounds too crazy for me.

Do you have an image of your MD box?

What does 3nm mean for your box? Half of any side?

Dr. Vitaly V. Chaban


On Mon, May 26, 2014 at 8:56 PM, ANDRES ADOLFO ORTEGA GUERRERO
 wrote:
> Hi dear Gromacs User,
> I have done a pulling simulation of a SWCNT against an ion channel(the
> SWCNT , and the ion channel pore's are the same), in order to study
> the interaction between SWCNT and the outside (extracellular side) of the
> channel,
> So i put the SWCNT about 3nm of distance from the ion channel, so the SWCNT
> starts going down straight (against ion channel) but there's a distance
> where the SWCNT just doesn´t go down, and starts to rotate in its own
> axis(Z in this case) , and tried to go down, just that it continue rotating
> and starts to turning,
>
> I was thinking that this behavior was due to the hydrophobic nature of the
> SWCNT ,
>
> i was wondering if you have any idea of this, or if this is ok, i tried a
> force of 800 and the result was the same
>
> pull= umbrella
> pull_geometry   = distance
> pull_dim= N N Y
> ;pull_vec1   = 0.0 0.0 1.0 ;
> pull_start  = yes
> pull_ngroups= 1
> pull_group0 = Protein
> pull_group1 =CNT
> pull_init1  = 0
> pull_rate1  = -0.1
> pull_k1 = 1000  ; kJ mol^-1 nm^-2
>
> thank you in advance
>
> Andres Ortega
> Universidad del Valle (Colombia)
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Re: [gmx-users] CNT ROTATION

[Dr. Vitaly Chaban]

provided that pulling forces are normally selected (much) larger than
the genuine forces in the simulated system, unfavorable interactions
are unlikely to cause the observed effect. however, rotation is
probably somehow geared by pulling energy. i looked though the movie -
it is like a nice helicopter.


Dr. Vitaly V. Chaban


On Tue, May 27, 2014 at 11:55 PM, Justin Lemkul  wrote:
>
>
> On 5/27/14, 11:25 AM, ANDRES ADOLFO ORTEGA GUERRERO wrote:
>>
>> Hi Dr Vitaly ,
>>
>> First 3nm it is not half of any side, i used the external amino acids from
>> the channel as a reference gruop, and 3nm is the distance from the SWCNT
>> tip's to the channel, but 6nm from the COM, my box has 19 nm in Z axis,
>>
>
> From what you describe, it sounds simply like the pulling force causes the
> CNT to interact unfavorably with the protein, such that the biasing force
> cannot actually move the CNT along the desired axis, instead dissipating the
> force in some bizarre ways.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA 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
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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Re: [gmx-users] Diferent Pressure Solvent

[Dr. Vitaly Chaban]

why do you need this weird setup?


Dr. Vitaly V. Chaban


On Wed, May 28, 2014 at 1:25 AM, Justin Lemkul  wrote:
>
>
> On 5/27/14, 6:52 PM, ANDRES ADOLFO ORTEGA GUERRERO wrote:
>>
>> Hi Dear Gromacs Users
>>
>> I was wondering if i want to simulate a SWCNT with water inside, it
>> possible , to run an MD with the inside water with a diffent pressure (2
>> Bar) , and the outside water and CNT a 1 bar?,
>> It is ok to use an index file, and use different pressure values with the
>> barostat i think this cant be done,
>> How could i done this?
>

>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA 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
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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Re: [gmx-users] Diferent Pressure Solvent

[Dr. Vitaly Chaban]

if you simulate adsorption of your molecule at 2 bar and then seal the
tube, then pressure inside tube will be 2 bar. in turn, you can
control pressure outside using the barostat.

though a difference between 1 bar and 2 bar in case of very spatially
small MD systems and therefore huge pressure fluctuations is probably
difficult to capture. maybe 1 bar and 100 bar will make more sense...


Dr. Vitaly V. Chaban


On Wed, May 28, 2014 at 6:20 PM, ANDRES ADOLFO ORTEGA GUERRERO
 wrote:
> I have this idea to try to "emulate" a chemical gradient,
>
> this is because i would like to see the diffusion of a molecule that it is
> caged in the SWCNT, an see if i can reproduce "a chemical gradient" in
> order to see a diffusion
> of the molecule,
>
> This idea is to try to model a chemical gradient confined in a SWCNT in
> order to get the diffusion of the molecule in an ion channel,
>
> I think the best way to do this maybe is to create a system, and be
> carefull this the position of ions
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Re: [gmx-users] CNT ROTATION

[Dr. Vitaly Chaban]

it is better to avoid rotation at this initial stage. if you
experience certain features in your finals PMFs which you cannot
explain, you will always be unsure where they arrive from. this hurts
your soul.



Dr. Vitaly V. Chaban


On Thu, May 29, 2014 at 9:41 PM, ANDRES ADOLFO ORTEGA GUERRERO
 wrote:
> Should i try instead different pull MD(changing the pbcatom, CNT's COM,
> velocity,force) , in order to get new configuration for an umbrella
> sampling simulation and a PMF in z Axis calculation, until i´ll get no
> rotation in the CNT?
> or can i used this MD, to get the configuration for the Umbrella Sampling??
>
> Thank you for your help and patience
>
> Andrés Ortega
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Re: [gmx-users] the water box become much larger in high temporature replicas after replica exchange simulation

[Dr. Vitaly Chaban]

> On Jun 5, 2014 8:34 AM, "#ZHANG HAIPING#"  wrote:
>>
>> Dear gromacs user：
>>
>> I have used follow .mdp to run the replica exchange simulation, after the
> simulation, I find the water box become much larger in high temporature
> replicas, can anyone tell me how to solve this? By the way, is it caused by
> the water box not large enough?


This means that your "high temperature" in REMD is higher than you
actually want it to be. Decrease it.


Dr. Vitaly V. Chaban
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Re: [gmx-users] Reactive force field

[Dr. Vitaly Chaban]

no.



Dr. Vitaly V. Chaban


On Mon, Jun 9, 2014 at 3:36 PM, Nilesh Dhumal  wrote:
> Hello,
>
> Could it possible to run the simulation with reactive force field using
> Gromacs?
>
>
> Nilesh
>
>
>
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Re: [gmx-users] Martini in Gromacs

[Dr. Vitaly Chaban]

where do you see errors?


Dr. Vitaly V. Chaban


On Tue, Jun 10, 2014 at 2:44 PM, Neha Gandhi  wrote:
> Hello,
>
> I am trying to run coarse grained MD in gromacs. I get following errors,
> should I reduce the time step? Your feedback is appreciated.
>
>
> NOTE 1 [file prod1.mdp]:
>   nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
>   nstcomm to nstcalcenergy
>
>
> NOTE 2 [file prod1.mdp]:
>   The Berendsen thermostat does not generate the correct kinetic energy
>   distribution. You might want to consider using the V-rescale thermostat.
>
>
> WARNING 1 [file prod1.mdp]:
>   For proper integration of the Parrinello-Rahman barostat, tau-p (2)
>   should be at least 20 times larger than nstpcouple*dt (0.2)
>
>
> NOTE 3 [file prod1.mdp]:
>   The switch/shift interaction settings are just for compatibility; you
>   will get better performance from applying potential modifiers to your
>   interactions!
>
>
> Generated 0 of the 780 non-bonded parameter combinations
> Excluding 1 bonded neighbours molecule type 'Protein_A'
> Excluding 1 bonded neighbours molecule type 'W'
> Excluding 1 bonded neighbours molecule type 'CL-'
>
> WARNING 2 [file topol.top, line 16]:
>   The bond in molecule-type Protein_A between atoms 1 BB and 3 BB has an
>   estimated oscillational period of 9.7e-02 ps, which is less than 5 times
>   the time step of 2.0e-02 ps.
>   Maybe you forgot to change the constraints mdp option.
>
>
> WARNING 3 [file prod1.mdp]:
>   For proper integration of the Berendsen thermostat, tau-t (0.5) should be
>   at least 5 times larger than nsttcouple*dt (0.2)
>
> Number of degrees of freedom in T-Coupling group Protein is 11517.00
> Number of degrees of freedom in T-Coupling group Other is 198744.00
> Reading Coordinates, Velocities and Box size from old trajectory
> Will read whole trajectory
> Last frame -1 time 5.000
> Using frame at t = 5 ps
> Starting time for run is 0 ps
>
> NOTE 4 [file prod1.mdp]:
>   This run will generate roughly 48891 Mb of data
>
>
> There were 4 notes
>
> There were 3 warnings
>
> ---
> Program grompp, VERSION 4.6.3
> Source code file: /ivec/build/gromacs-4.6.3/src/kernel/grompp.c, line: 1910
>
> Fatal error:
> Too many warnings (3), grompp terminated.
> If you are sure all warnings are harmless, use the -maxwarn option.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> Here is the mdp file
> ; RUN CONTROL PARAMETERS =
> integrator   = md
> ; start time and timestep in ps =
> tinit= 0.0
> dt   = 0.020
> nsteps = 12500
> ; 125 mio steps x 20fs = 2500ns = 10* microsec
> ; number of steps for center of mass motion removal
> nstcomm  = 1
> ; group(s) for center of mass motion removal
> comm-grps= Protein Other
>
> ; OUTPUT CONTROL OPTIONS =
> ; Output frequency for coords (x), velocities (v) and forces (f) =
> nstxout  = 5000
> nstvout  = 5000
> nstfout  = 0
> ; Output frequency for energies to log file and energy file =
> nstlog   = 5000
> nstenergy= 5000
> ; Output frequency and precision for xtc file =
> nstxtcout= 5000
> xtc_precision= 100
> ; This selects the subset of atoms for the xtc file. You can =
> ; select multiple groups. By default all atoms will be written. =
> xtc-grps = System
> ; Selection of energy groups =
> energygrps   = Protein Other
>
> ; NEIGHBORSEARCHING PARAMETERS =
> ; nblist update frequency =
> nstlist  = 10
> ; ns algorithm (simple or grid) =
> ns_type  = grid
> ; Periodic boundary conditions: xyz or none =
> pbc  = xyz
> ; nblist cut-off =
> rlist= 1.4
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW =
> ; Method for doing electrostatics =
> coulombtype  = Shift
> rcoulomb_switch  = 0.0
> rcoulomb = 1.2
> ; Dielectric constant (DC) for cut-off or DC of reaction field =
> epsilon_r= 15
> ; Method for doing Van der Waals =
> vdw_type = Shift
> ; cut-off lengths=
> rvdw_switch  = 0.9
> rvdw = 1.2
> ; Apply long range dispersion corrections for Energy and Pressure =
> DispCorr = No
>
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS =
> ; Temperature coupling   =
> tcoupl   = Berendsen
> ; Groups to couple separately =
> tc-grps  = Protein Other
> ; Time constant (ps) and reference temperature (K) =
> tau_t= 0.5  0.5
> ref_t= 310 310
> ; Pressure coupling  =
> Pcoupl   = Parrinello-Rahman
> Pcoupltype   

Re: [gmx-users] how many groups shall I use to control the temperature?

[Dr. Vitaly Chaban]

There is no rule regarding how many thermostats per system one needs.

Often people choose separate thermostats for parts of system, which
exhibit different mobility. I do not see any connection to functional
forms of the interactions and, therefore, to force fields.


Dr. Vitaly V. Chaban


On Thu, Jun 12, 2014 at 2:33 PM, 陈功  wrote:
> Thanks a lot, Justin. I do CG simulation using Martini force field. So maybe 
> I can find some useful infomation on the forum of martini.
> Thanks :)
>
>
>
>
>
> From: Justin Lemkul
> Date: 2014-06-12 17:44
> To: gmx-users
> Subject: Re: [gmx-users] how many groups shall I use to control the 
> temperature?
>
>
> On 6/12/14, 2:37 AM, 陈功 wrote:
>> Dear justin,
>>   I have doubts that whether I should use two groups to control the 
>> temperature or just one since there are just 604 hundred Protein beads and 
>> 6+ solvent beads. It is said that two groups are more accurate but when 
>> when i split them into two groups "Protein nonProtein", I found that 
>> fluctulation of temperature in group "Protein" are obvious, Im afraid that 
>> would have an effect on accuracy on my simulation results. So how many 
>> groups shall I use to control the temperature?
>
> What protocol is used in published studies similar to what you're doing?  
> Small
> groups will have larger fluctuations in temperature, that's a given.  I don't 
> do
> CG simulations, so I don't know how such groups are commonly treated.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA 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
>
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> http://mackerell.umaryland.edu/~jalemkul
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> ==
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Re: [gmx-users] How to exit cluster during the simulation

[Dr. Vitaly Chaban]

turn off your pc

Dr. Vitaly V. Chaban


On Sun, Jun 15, 2014 at 5:53 AM, Batdorj Batsaikhan
 wrote:
> Dear GMX users,
>
> I am a new user of gromacs on cluster. I use putty to connect to the cluster. 
> I have a problem. How to exit cluster during the simulation?
>
> My last command is " mpirun -np 8 mdrun_mpi ... "
>
> in the past,  I clicked "X" button of putty, mdrun did not finished.
>
> Thank you.
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Re: [gmx-users] Regarding lipid topology

[Dr. Vitaly Chaban]

Of course, no. You need to adjust your topology (force field?) to
distinguish between cis- and trans- states.


Dr. Vitaly V. Chaban


On Mon, Jun 16, 2014 at 11:03 AM, Venkat Reddy  wrote:
> Dear all,
> I want to simulate a membrane protein system. My membrane is composed of
> DOPC (cis isomer) and DEPC (trans isomer). I have downloaded DOPC topology
> from lipidbook website. Since DOPC and DEPC are isomers, can I use the
> topology of DOPC for DEPC also?
>
> Thank and regards
>
> Venkat Reddy Chirasani
> PhD student
> Laboratory of Computational Biophysics
> Department of Biotechnology
> IIT Madras
> Chennai
> INDIA-600036
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Re: [gmx-users] More suitable force field and water model

[Dr. Vitaly Chaban]

There is no best combination.

The parameters for water for your solute must be derived using
physically equivalent procedures.
That's all.

Dr. Vitaly V. Chaban


On Thu, Jun 19, 2014 at 11:59 AM, Mohsen Ramezanpour
 wrote:
> Dear Gromacs Users,
>
> I have read some articles about the more appropriate combination of force
> field and water model for different simulations of interest.
> It is confusing and too difficult to decide which combination is the best
> one. Besides according to articles I read, I am in doubt now and not sure
> which combination should I choose.
>
> As I understood, the SPC and TIP4P are recommended for biomolecular
> simulations and some authors have also recommended SPC.
>
> Although SPC/E seems the best one in non-polarizable models for bulk
> properties of water but for different quantities of interest such as
> hydration free energy, hydration enthalpy, entropy, heat capacities etc.
> some special combinations will be more appropriate.
>
> I found that although using a FF+water model will result in a precise
> enough quantity but we can not rely on some other quantities of our
> simulation!
> By this I mean, If we are interested in hydration free energy, the best
> option seems to be Gromos 53a6 and SPC or SPC/E model. But if we are
> interested in other quantities as well, other combinations will be
> preferred.
>
>
> In fact I am interested in Protein-ligand binding free energy and also its
> Enthalpy and Entropy contributions as well.
> I guess in this case it is better to choose Gromos+SPC or SPC/E. But I am
> not sure.
>
> I think it is also related to properties of our system components (charge,
> etc.). for example for sugars or lipids.
>
> Is there any article which has compared these in details? Please let me
> know.
> any suggestion is appreciated in advance
>
>
> Best Regards
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Re: [gmx-users] NPT MD and Berendsen

[Dr. Vitaly Chaban]

thermodynamic ensemble has nothing to do with an average pressure value.

Dr. Vitaly V. Chaban


On Mon, Jun 23, 2014 at 7:50 AM, Chetan Mahajan  wrote:
> Dear All,
>
> I am using Berendsen barostat and thermostat for NPT equilibration MD run
> at 1 atm and 300 K. While it runs fine, average pressure at the end of the
> run is 19 bar. I am confused whether this is way off 1 atm target, or is
> justified recalling gromacs manual that says Berendsen barostat does not
> yield correct thermodynamic ensemble.
>
> IN addition, initial box elongates to have space at both ends in
> z-direction as can be seen in following link:
>
> https://www.dropbox.com/sh/dahnyy3zy6vb1xh/AAD5ppxrm18rB3DHZ0Qji0qva
>
> Again, I am not sure if this is a case for concern or just artifact of
> using Berendsen.
>
> Is Parrinello-Rahman better than Berendsen, even for initial NPT
> equilibration?
>
> Thanks
> Chetan
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Re: [gmx-users] Charges & non-bonded interaction values usage in different force fields

[Dr. Vitaly Chaban]

Can you perhaps kindly explain us how "charges and non-bonded
interaction values" were "experimentally determined"?

Dr. Vitaly V. Chaban


On Tue, Jun 24, 2014 at 10:37 AM, Rj  wrote:
> Dear all,
>
>
> Experimentally determined charges and non-bonded interaction values for 
> ligand atoms ( Written in charmm) can be used directly in gromacs provided 
> charmm27.ff ? or does it need any conversion to use it in gromacs based 
> charmm27.ff?
>
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Re: [gmx-users] Carbon monoxide topology

[Dr. Vitaly Chaban]

In my opinion, it is an acceptable solution to take these parameters as is.

Especially, if you write some wise words about philosophy of FF
compatibility/trasferability and pairwise interactions for your
methodology section.


Dr. Vitaly V. Chaban


On Wed, Jun 25, 2014 at 8:02 AM, Mark Abraham  wrote:
> If you're happy that such parameters might work with your intended force
> field, then you only need to build them into a topology. Assuming you have
> some GROMACS experience, check out the relevant parts of chapters 4 and 5
> of the manual.
>
> Mark
> On Jun 25, 2014 4:01 AM, "라지브간디"  wrote:
>
>> Dear Dr. Vitaly V. Chaban,
>>
>>
>> The charges and non-bonded interactions of Carbon monoxide are set to give
>> approximate agreement with the experimental dipole & quardrupole moments (
>> J.E. Straub, M. Karplus, Chemical Physics, 1991).
>>
>>
>> According to this article, with the specific point charges and LJ
>> parameters fit to give good agreement with the multipole moments of CO as
>> well as lattice constant for the Myoglobin with CO structure ( Written for
>>
>>
>> Charmm ff)
>>
>>
>> Hence, i would like to know how do i interpret this values in charmm27 ff
>> in gromacs? Thank you for your concern.
>> Msg: 3
>> Date: Tue, 24 Jun 2014 11:26:02 +0200
>> From: "Dr. Vitaly Chaban" 
>> To: gmx-us...@gromacs.org
>> Subject: Re: [gmx-users] Charges & non-bonded interaction values usage
>> in different force fields
>> Message-ID:
>> 
>> Content-Type: text/plain; charset=UTF-8
>>
>> Can you perhaps kindly explain us how "charges and non-bonded
>> interaction values" were "experimentally determined"?
>>
>> Dr. Vitaly V. Chaban
>>
>> On Tue, Jun 24, 2014 at 10:37 AM, Rj  wrote:
>> > Dear all,
>> >>
>> > Experimentally determined charges and non-bonded interaction values for
>> ligand atoms ( Written in charmm) can be used directly in gromacs provided
>> charmm27.ff ? or does it need any conversion to use it in gromacs based
>> charmm27.ff?
>> >
>>
>>
>>
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Re: [gmx-users] EDLC simulation using Gromacs

[Dr. Vitaly Chaban]

It is very easy. You apply an electric field and observe how DL is forming.

Have fun.

Dr. Vitaly V. Chaban


On Fri, Jun 27, 2014 at 3:14 PM, Andy Chao  wrote:
> Dear Users,
>
> Would you please suggest a few examples of using GROMACS to simulate an
> EDLC device?
>
> Thanks a lot!
>
> Andy
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Re: [gmx-users] CNT with BN co doping

[Dr. Vitaly Chaban]

Simulation of doped nanostructures is much more complicated than
described below. You must account for the effect of your new fragments
on electron density of the entire nanostructure. There is enough
evidence that an additive approach fails here.

Good luck.

Dr. Vitaly V. Chaban


On Mon, Jun 30, 2014 at 11:45 AM, akari karin  wrote:
> I am trying to simulate carbon nanotubes with some doping. The way i am
> doping my nanotube is by B-N codoping.
>
> i generated the structure but stuck with the topology. i know i need to
> have the bonded and nonbonded interaction parameters for Boron and Nitrogen
> to do the work but i dont understand how i can get those.
>
> i am using the modified oplsaa force field for the simulation of CNT
> structure. will the default parameters in the oplsaa be okay for my
> simulation? if not how can i get the parameters?
>
> thanks in advance
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Re: [gmx-users] How to calculate Box Vectors in the last line of the .gro file?

[Dr. Vitaly Chaban]

You need to set the box vectors with respect to system density or
anticipated system density.


Dr. Vitaly V. Chaban


On Sun, Jun 29, 2014 at 9:06 PM, Todor Antonijevic  wrote:
> Hi,
>
> I cannot obtain the last line (box vectors *1.82060 1.82060 1.82060*) of
> the .gro file.
>
> *Can anyone explain me how the last line is calculated?*
>
> The example is from the manual:
>
> "MD of 2 waters, t= 0.0
>
> 6
> 1WATER  OW11   0.126   1.624   1.679  0.1227 -0.0580  0.0434
> 1WATER  HW22   0.190   1.661   1.747  0.8085  0.3191 -0.7791
> 1WATER  HW33   0.177   1.568   1.613 -0.9045 -2.6469  1.3180
> 2WATER  OW14   1.275   0.053   0.622  0.2519  0.3140 -0.1734
> 2WATER  HW25   1.337   0.002   0.680 -1.0641 -1.1349  0.0257
> 2WATER  HW36   1.326   0.120   0.568  1.9427 -0.8216 -0.0244
>
>*1.82060 1.82060 1.82060*"
>
> Thank you very much
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Re: [gmx-users] Questions regarding converting .GRO files to .TOP files

[Dr. Vitaly Chaban]

I believe x2top works nice only when you have a single molecule in a
structure file.

Perhaps, the algorithm wants to connect molecules, which are not
actually connected, and goes crazy, but it is just a guess.


Dr. Vitaly V. Chaban


On Mon, Jun 30, 2014 at 5:46 AM, Andy Chao  wrote:
> Dear GROMACS users:
>
> I have a few questions about converting the .GRO files to .TOP files.  I
> first used Python to create a sheet of graphene layer by using the
> following Python codes:
>
> from ase import *
> from ase.structure import graphene_nanoribbon
> from ase io.import*
> gnr1 = graphene_nanoribbon(8,8, type='armchair')
> write('graphene.pdb', gnr1, format='pdb')
>
> Second, I used the following codes to convert the PDB file to GRO file for
> the cathode layer:
>
> editconf -f graphene.pdb -o graphene_cathode.gro
>
> Third, I used the following codes to convert the PDB files to GRO file for
> the anode layer:
>
> editconf -f graphene.pdb -translate 0 5.0 -o graphene_anode.gro
>
> Fourth, I combined the cathode layer and the anode layer to one complete
> structure according to the following code:
>
> genbox -cs graphene_cathode.gro -cp graphene_anode.gro -maxsol 5000 -box 3
> 1 3 -o electrodes.gro
>
> Fifth, I converted the electrode gro file to top file according to the
> following code:
>
> g_x2top -f electrodes.gro -ff cnt_oplsaa -o device.top
>
> GROMACS showed that there are carbon atoms force field that can not be
> found in the atomname2type.n2t file.
>
> part of the error message is shown as the following:
>
> Can not find forcefield for atom C-447 with 6 bonds
> Can not find forcefield for atom C-448 with 5 bonds
>
> Fatal error:
>
> Could only find a forcefield type for 364 out of 512 atoms.
>
> My atomname2type.n2t file consists of the following:
>
> C   opls_145  -0.12   12.011 3 C   0.150  C  0.150   H   0.108
> C   opls_145  -0.12   12.011 3 C   0.133  C  0.150   O  0.140
> C   opls_145   0.0 12.011 3 C   0.140  C  0.140   C  0.140
> C   opls_145   0.0 12.011 2 C   0.140  C  0.140
>
> However, the TOP files for the cathode layer or the anode layer can be
> converted from the GRO files without any error as the following:
>
> g_x2top -f graphene_cathode.gro -ff cnt_oplsaa -o graphene_cathode.top
> g_x2top -f graphene_anode.gro -ff cnt_oplsaa -o graphene_anode.top
>
> can people explain why?  What is the reason behind the error message that I
> got when converting the GRO file of two combined layer of graphene to the
> TOP file while the same atomname2type.n2t file is used?
>
>
> Thank you very much!
>
> Andy
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Re: [gmx-users] CNT with BN co doping

[Dr. Vitaly Chaban]

I do not believe that your methodological solution is physically relevant

Dr. Vitaly V. Chaban


On Mon, Jun 30, 2014 at 12:33 PM, akari karin  wrote:
> thanks Dr. Vitaly V. Chaban for your reply.
>
> i already simulated the CNT without doping and i have developed a structure
> with the doped CNT.
>
> now if i add the dopant atoms in my forcefield file (for example, in my case
> i add nonbonded parameters to my ffnonbond.itp and bonded parameters to my
> bonded.itp and so on) will it be the correct way to do the simulation?
>
> and it would be very nice if you could explain the statement,
>
> "You must account for the effect of your new fragments on electron density
> of the entire nanostructure."
>
> a little bit further.
>
> thanks for your time
>
>
>
>
> On Mon, Jun 30, 2014 at 4:01 PM, Dr. Vitaly Chaban 
> wrote:
>>
>> Simulation of doped nanostructures is much more complicated than
>> described below. You must account for the effect of your new fragments
>> on electron density of the entire nanostructure. There is enough
>> evidence that an additive approach fails here.
>>
>> Good luck.
>>
>> Dr. Vitaly V. Chaban
>>
>>
>> On Mon, Jun 30, 2014 at 11:45 AM, akari karin 
>> wrote:
>> > I am trying to simulate carbon nanotubes with some doping. The way i am
>> > doping my nanotube is by B-N codoping.
>> >
>> > i generated the structure but stuck with the topology. i know i need to
>> > have the bonded and nonbonded interaction parameters for Boron and
>> > Nitrogen
>> > to do the work but i dont understand how i can get those.
>> >
>> > i am using the modified oplsaa force field for the simulation of CNT
>> > structure. will the default parameters in the oplsaa be okay for my
>> > simulation? if not how can i get the parameters?
>> >
>> > thanks in advance
>> > --
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>> >
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Re: [gmx-users] Regarding lipid topology

[Dr. Vitaly Chaban]

Unlikely anything on top of dihedrals.

Try to use VMD to see if the lipid molecules look as you like.

I do not have to handle lipid isomer simulations, fortunately.


Dr. Vitaly V. Chaban


On Wed, Jul 2, 2014 at 7:33 PM, Venkat Reddy  wrote:
> Thank you Sir. Sorry for the late reply. So, the changes like dihedral
> angle for C8-C9=C10-C11 should be 180 instead of 0 in trans state. Are
> there any other adjustments I should make to build the trans lipid isomer
> topology from cis? Thank you for your valuable time and concern.
>
>
> On Mon, Jun 16, 2014 at 4:44 PM, Dr. Vitaly Chaban 
> wrote:
>
>> Of course, no. You need to adjust your topology (force field?) to
>> distinguish between cis- and trans- states.
>>
>>
>> Dr. Vitaly V. Chaban
>>
>>
>> On Mon, Jun 16, 2014 at 11:03 AM, Venkat Reddy 
>> wrote:
>> > Dear all,
>> > I want to simulate a membrane protein system. My membrane is composed of
>> > DOPC (cis isomer) and DEPC (trans isomer). I have downloaded DOPC
>> topology
>> > from lipidbook website. Since DOPC and DEPC are isomers, can I use the
>> > topology of DOPC for DEPC also?
>> >
>> > Thank and regards
>> >
>> > Venkat Reddy Chirasani
>> > PhD student
>> > Laboratory of Computational Biophysics
>> > Department of Biotechnology
>> > IIT Madras
>> > Chennai
>> > INDIA-600036
>> > --
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>> posting!
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>
>
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> With Best Wishes
> Venkat Reddy Chirasani
> PhD student
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> Department of Biotechnology
> IIT Madras
> Chennai
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Re: [gmx-users] Graphene topology file

[Dr. Vitaly Chaban]

Graphene topology is like for tube, so

C  C
C ... C ... C
C  C  C   C

to the N2T file and you are done.


Dr. Vitaly V. Chaban


On Wed, Jul 2, 2014 at 5:29 PM, Justin Lemkul  wrote:
>
>
> On 7/2/14, 9:56 AM, #SUKRITI GUPTA# wrote:
>>
>> Dear all,
>>
>>
>> I want to simulate graphite in water, for which i am trying to create a
>> topology file for graphite. As its .rtp file cannot be written correctly, i
>> tried to use g_x2top command following the steps given in following
>> tutorial.
>>
>> http://chembytes.wikidot.com/grocnt
>>
>>
>> But I think this tutorial is quite old and hence suitable for older
>> version of gromacs as it still uses FF.dat file. Moreover if i am trying to
>> make a new forcefield directory with name graphite_oplsaa containing the
>> modified files like .n2t,.rtp and .itp, its giving me an error that "Could
>> not find force field 'graphite_oplsaa' in current directory, install tree or
>> GMXDATA path". When I try to add this forcefield in original path ie.
>> user/share/gromacs/top, it does not allow me to do that as i am not the
>> administrator. Can anyone please let me know how to create the topology
>> file. I require 3 graphene sheets with pbc. I have created the .pdb file
>> using nanobuilder in vmd.
>>
>
> The tutorial is indeed outdated but the logic is fairly sound.  You don't
> have to modify anything in $GMXLIB (system-wide); you can just create an
> .n2t file in the working directory and it will override the one at the force
> field level.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA 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
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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Re: [gmx-users] gromacs Bug?

[Dr. Vitaly Chaban]

unless your pc is kidding you, there is a problem with index group assignment.

Dr. Vitaly V. Chaban


On Sat, Jul 19, 2014 at 3:56 AM, ANDRES ADOLFO ORTEGA GUERRERO
 wrote:
> Hi dear Gromacs  users, i would like to report something maybe could be a
> bug or a mistake of me , you´ll see, i run an MD of a System with CNT
> Protein Water and ions, i use a index.ndx file, my CNT doestn´t have any
> charges, but when i check the Coul SR CNT-CNT there were really huge,
>
> so i start a process and run different MD in order to get the problem, and
> , the only way i could Coul SR CNT-CNT 0 as is supposed to be, was when i
> do not use an index file,
> with different simulation where i use the index.ndx file, my energy are
> different ,
>
> Thank You
>
> Andres
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Re: [gmx-users] about cos-accelation

[Dr. Vitaly Chaban]

1) g_energy -vis is always Einstein

g_energy and then select 1/visc term - NE method.


2) I do not think it makes physical sense to distinguish between
viscosities in a mixture because of the definition of viscosity.
Specifying cos-acc will supply extra energy to all particles.


3) Rigorously, one must use a set of values and extrapolate
viscosities to zero-acceleration. Some cunning researchers use a
single small value, though, and say that the uncertainty coming from
extrapolation is within viscosity error bars.

0.05 is a reasonable acceleration to start with, but it depends on the
simulated system.

4) The bug with volume was in the earlier 4th versions. I believe that
it was fixed around ver. 4.5.


Good luck.


Dr. Vitaly V. Chaban






On Wed, Jul 23, 2014 at 5:18 AM, Hyunjin Kim  wrote:
> Dear,
>
> As I understand, in order to calculate viscosity in Gromacs, I can use
> "g_energy -f -vis ..." using .edr file after simulation.
>
> Regarding this, I have four questions :
>
> 1. Regardless of including cos-acceleration command in my .mdp file,
> I can obtain viscosity. This means that if I include cos-acceleration
> during simulation, then the viscosity value is obtained from acceleration
> (or non-eq method). Otherwise, the value is calculated using Einstein
> relation. Am I right? Or will "g_energy -vis" always yields viscosity
> using Einstein relation.
>
> 2. If I use mixture of molecules in the system, then can I calculate
> viscosity for each molecule in the system?
>
> 3. I have checked mailing list, it looks people use different
> cos-acceleration values, e.g., 0.1, 0.25, or 0.5 nm/ps^2. I wonder how
> people choose the values? Does viscosity depend on this value?
>
> 4. If I use Gromacs 4.6.1 or higher, then is the bug for volume division
> correct?
>
>
> Hopefully, my questions are clear. Thanks a lot for your support in advance.
>
>
>
>
>
>
>
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Re: [gmx-users] Molecular Solid PBC problem

[Dr. Vitaly Chaban]

You can see in the topology file whether gromacs wrote down bonds
responsible for periodicity.

Coordinate file says nothing in this regard.


Good luck.


Dr. Vitaly V. Chaban





On Wed, Jul 23, 2014 at 1:53 AM, Guilherme Duarte Ramos Matos
 wrote:
> Dear GROMACS user community,
>
> I'm working with molecular dynamics of molecular solids and I am having
> trouble to set up the calculations.
>
> I got the crystal structure's pdb file from the Cambridge Database and used
> editconf to generate the coordinate file. The topology file is really
> simple: it just carries the hamiltonian of an Einstein crystal, that is,
> harmonic potentials binding each atom of the molecule to its lattice
> position. The relevant part of the mdp file is:
>
> ; NEIGHBORSEARCHING PARAMETERS
> ; nblist update frequency
> nstlist  = 1
> ; ns algorithm (simple or grid)
> ns_type  = grid
> ; Periodic boundary conditions: xyz (default), no (vacuum)
> ; or full (infinite systems only)
> pbc  = xyz
> ; nblist cut-off
> rlist= 1.0
>
> Unfortunately, after running grompp, I get the following warning:
>
>  WARNING 1 [file molecule_ideal.top, line 351]:
>   10116 non-matching atom names
>   atom names from molecule_ideal.top will be used
>   atom names from input.gro will be ignored
>
> The funny and worrying part of this problem is that all the atom types were
> changed in the output of mdrun. The simulation just didn't crash because of
> the hamiltonian used. I investigated a little bit and it seemed that
> GROMACS was not able to connect the fragments in the wall to their
> neighboring periodic copies. That happened because fragments were numbered
> as distinct molecules. Check this small portion of the coordinate file:
>
>35RES C1  211   0.017   5.561   4.241
>35RES N1  212   0.033   5.362   4.363
>35RES O1  213   0.145   5.367   4.163
>35RES C2  214   0.074   5.421   4.245
>35RES H1  215   0.057   5.283   4.386
>35RES H3  216   0.087   5.628   4.238
>36RES C1  217   0.017   5.561   5.526
>36RES N1  218   0.033   5.362   5.648
>36RES O1  219   0.145   5.367   5.448
>36RES C2  220   0.074   5.421   5.530
>36RES H1  221   0.057   5.283   5.671
>36RES H3  222   0.087   5.628   5.523
>37RES C1  223   0.017   5.561   6.811
>37RES N1  224   0.033   5.362   6.933
>37RES O1  225   0.145   5.367   6.733
>37RES C2  226   0.074   5.421   6.815
>37RES H1  227   0.057   5.283   6.956
>37RES H3  228   0.087   5.628   6.808
>38RES C1  229   0.753   0.786   1.671
>38RES N1  230   0.770   0.587   1.793
>38RES O1  231   0.882   0.592   1.593
>38RES C2  232   0.811   0.646   1.675
>38RES O2  233   0.636   0.631   1.973
>38RES C3  234   0.687   0.665   1.868
>38RES C4  235   0.672   0.798   1.799
>38RES H1  236   0.794   0.508   1.816
>38RES H2  237   0.696   0.797   1.593
>38RES H3  238   0.824   0.852   1.668
>38RES H4  239   0.707   0.870   1.855
>38RES H5  240   0.579   0.817   1.779
>
> The molecule number 38 has 12 atoms and is inside the walls while 35, 36
> and 37 have 6 atoms each, represent similar fragments, along the wall but
> are accounted as isolated molecules.
>
> Does anyone have a suggestion to help me with this problem?
> Thank you in advance.
>
> ~ Guilherme
>
> *
> Guilherme D. R. Matos
> Graduate Student at UC Irvine
> Mobley Group
>
> *
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Re: [gmx-users] Angle group

[Dr. Vitaly Chaban]

Use g_angle and your index file must contain triples of the involved atoms.

if I remember correctly, this route provides a gaussian-type
probability distribution, i.e. not evolution vs. time.


Dr. Vitaly V. Chaban




On Wed, Jul 23, 2014 at 9:53 AM, Cyrus Djahedi  wrote:
> Hi!
> Im simulating the stretching of a cellulose fibril in the longitudinal plane. 
> It's made up of 16 polymers chains that are 10 cellobiose units in length, 
> and each cellobiose unit is connected through a glucosidic bond. Lets say I 
> want to get an average value of the angle that forms between the central 
> oxygen atom and the two flanking carbon atoms for every glucosidic bond in 
> the fibril, how should I do this? / Cyrus
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Re: [gmx-users] Lennard jones parameters for ions

[Dr. Vitaly Chaban]

Ionic and atomic radii are the same..? Wow!

You should reparametrize Fe(+++) obviously.
Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН


On Fri, Jul 25, 2014 at 1:39 PM, #SUKRITI GUPTA#
 wrote:
> Dear Gromacs users,
>
>
> I wanted to simulate metal ions in gromacs. For Fe+2, I have lj potential 
> parameters already defined in OPLSAA forcefield, so I wanted to know if I 
> want to add FE+3 in my simulation, then the LJ parameters for it will be 
> different from that of Fe+2 or same?
>
>
> I thought it will be same because vander waals radii is defined for a element 
> and not ion, hence it will be same for Fe or Fe+2 or Fe+3.
>
>
> Regards
>
> Sukriti
>
>
> [https://wis.ntu.edu.sg/graphics/tms/ntulogofit2.gif]
>
> Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | 
> Nanyang Technological University
> N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798
> Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | 
> Web:erian.ntu.edu.sg
>
>
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Re: [gmx-users] maximum energy in ipnic liquid

[Dr. Vitaly Chaban]

There is no "command", but your can obviously compute formation energy
of your structure.


Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН


On Mon, Jul 28, 2014 at 6:05 PM, Andy Chao  wrote:
> Dear gromacs users:
>
> is there any gromacs command that can allow us to compute the maximum
> allowable energy that can be sustained on an ionic liquid structure?
>
>
> in other words, instead of energy minimization, we would like to
> compute maximum energy under stability.
>
> Thanks!
>
> Andy
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Re: [gmx-users] Details about using g_wham

[Dr. Vitaly Chaban]

Unless you symmetrize the PMF before output, it should be along an
entire box side.

You do not specify how you pulled your molecule; therefore, it is
impossible to suggest further.


Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН


On Tue, Jul 29, 2014 at 1:42 AM, Yoo Chan Myung  wrote:
> Dear GMX-Users,
>
> I’m trying to obtain free energy profile of small molecule penetration
> through POPC membrane.
>
> To do that, many researchers simulate using Umbrella Sampling with G_Wham
> analysis.
>
> (Reference : 'convergence of free energy profile of coumarin in lipid
> bilayer’, Michal Otypeka)
>
>
> Most of x-axis(Distance from the middle of the lipid bilayer) of free
> energy profile show minus to plus x-axis.
>
> In my case, I have no idea how to obtain the g_wham results with region
> from minus to plus of membrane(x-axis).
> ($ g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal)
>
> I always get an energy profile which is raged from 0 to 3 for x-axis, not
> in minus.
>
> Is there any options on g_wham?
>
> Many thanks,
>
> Yoochan
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Re: [gmx-users] Error in methanol simulation

[Dr. Vitaly Chaban]

One MeOH molecule has run away from your PDB file.

Maybe something wrong with formatting?


Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН




On Sat, Aug 2, 2014 at 12:09 AM, Deepak Ojha  wrote:
> Dear gmx_users
> I am trying to do a simulation of methanol using the topology file from
> virtualchemistry.org.
> I created the topology file as given below
>
> ; Include forcefield parameters
> #include "methanol.itp"
>
> [ system ]
> methanol
> [ molecules ]
> methanol 108
>
> however when I do energy minimization grompp -f em.mdp -c pure.pdb -p
> test1.top -o em.tpr
> I get
>  Excluding 3 bonded neighbours molecule type 'methanol'
> Excluding 3 bonded neighbours molecule type 'methanol'
> processing coordinates...
>
> ---
> Program grompp, VERSION 4.0.7
> Source code file: ../../../../src/kernel/grompp.c, line: 362
>
> Fatal error:
> number of coordinates in coordinate file (pure.pdb, 648)
>  does not match topology (test1.top, 654)
> Any suggestions?
>
> --
> DeepaK Ojha
> School Of Chemistry
>
> "Selfishness is not living as one wishes to live, it is asking others to
> live as one wishes to live"
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Re: [gmx-users] linking lipid covalently to protein...

[Dr. Vitaly Chaban]

Nohow.

Because the peptide is not covalently bound to the lipid.


Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН




On Tue, Aug 12, 2014 at 6:57 PM, Ozbil, Mehmet  wrote:
> Hello,
>
>
> I am trying to run a GROMACS simulation with few amino acids covalently bound 
> to Palmitoyl-linoleylphosphatidylcholine molecules., by using GROMOS ff. I 
> found the lipid structure and parameters on Tieleman`s website, but I don`t 
> know how to get the parameters for covalently bound molecule. Can you suggest 
> any tutorial or any documentation? ? Thank you.
>
>
> Best,
>
> Mehmet Ozbil
>
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Re: [gmx-users] changing the viscosity of water in a simulation

[Dr. Vitaly Chaban]

On Tue, Sep 2, 2014 at 10:59 AM, soumadwip ghosh
 wrote:
> Hello,
>
>   I am a newbie to MD simulation. We are working in the direction of
> finding the molecular origin of internal friction of protein folding. For
> this we have to run folding simulations at different solvent viscosity and
> plot protein reconfiguration time against solvent viscosity. Currently, we
> have been using TIP3P water molecules for simulations run on GROMACS 4.5.6.
> I wwill be highly grateful if someone tells me how to change the viscosity
> of water.


To change water viscosity, you must be assigned as God.

Pick up another FFM.


Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН


>
> Best,
> Soumadwip.
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Re: [gmx-users] the growth of the molecule

[Dr. Vitaly Chaban]

Why not? Your interaction potential is responsible for everything.



Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН


On Mon, Sep 15, 2014 at 7:27 PM, Александр Селютин  wrote:
> Can the gromacs simulate the growth of the molecule?
> For example, does it allow to add units to the polymer chain at certain
> times?
> More specifically, it is the increase the chain length of the polyethylene.
>
> Thanks!
> --
> Regards,
> Alexander Selyutin
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Re: [gmx-users] Freezing problem

[Dr. Vitaly Chaban]

probably there should be three "freeze values" standing for Cartesions
directions. What I see below is "YYY" with no spaces between.


Dr. Vitaly V. Chaban


On Fri, Nov 22, 2013 at 1:56 PM, Debashis Sahu
 wrote:
> Dear all,
>I can not freeze a group in mdrun in gas phase. Actually the
> following error is coming in the grompp step
>
> Program grompp, VERSION 4.6.3
> Source code file: /compile/gromacs-4.6.3/src/kernel/readir.c, line: 3192
>
> Fatal error:
> Invalid Freezing input: 1 groups and 1 freeze values
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> I have tried also by taking the index file in grompp step, but same error
> coming. My index file and mdp file are listed below. I want to freeze ABC
> group while DDD will be free. In the topology I have inserted the molecule
> DDD as DDD.itp..If any mistake in the files there, plz help me.
>
> *index.ndx file:*
>
> [ System ]
>123456789   10   11   12   13   14   15
>   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30
>   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45
>   46   47   48   49   50   51   52   53   54   55   56   57   58   59   60
>   61   62   63   64   65   66   67   68   69   70   71   72   73   74   75
>   76   77   78   79   80   81   82   83   84   85   86   87   88   89   90
>   91   92   93   94   95   96   97   98   99  100  101  102  103  104  105
>  106  107  108  109  110  111  112  113  114  115  116  117  118  119  120
>  121  122  123  124  125  126  127  128  129
> [ Other ]
>123456789   10   11   12   13   14   15
>   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30
>   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45
>   46   47   48   49   50   51   52   53   54   55   56   57   58   59   60
>   61   62   63   64   65   66   67   68   69   70   71   72   73   74   75
>   76   77   78   79   80   81   82   83   84   85   86   87   88   89   90
>   91   92   93   94   95   96   97   98   99  100  101  102  103  104  105
>  106  107  108  109  110  111  112  113  114  115  116  117  118  119  120
>  121  122  123  124  125  126  127  128  129
> [ ABC ]
>123456789   10   11   12   13   14   15
>   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30
>   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45
>   46   47   48   49   50   51   52   53   54   55   56   57   58   59   60
>   61   62   63   64   65   66   67   68   69   70   71   72   73   74   75
>   76   77   78   79   80   81   82   83   84   85   86   87   88   89   90
>   91   92   93   94   95   96   97   98   99  100  101  102  103  104  105
>  106  107  108  109  110  111  112  113  114  115  116  117  118  119  120
>  121  122  123  124  125  126
> [ DDD ]
>  127  128  129
>
> *mdp file:*
>
> title = NVT equilibration
> define = -DPOSRES ; position restrain the solute
> ; Run parameters
> integrator = md ; leap-frog integrator
> nsteps = 5 ; 2 * 5 = 100 ps
> dt = 0.002 ; 2 fs
> ; Output control
> nstxout = 100 ; save coordinates every 0.2 ps
> nstvout = 100 ; save velocities every 0.2 ps
> nstenergy = 100 ; save energies every 0.2 ps
> nstlog = 100 ; update log file every 0.2 ps
> ; Bond parameters
> continuation = 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 = 1.0 ; short-range neighborlist cutoff (in nm)
> rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
> rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
> pme_order = 4 ; cubic interpolation
> fourierspacing = 0.16 ; grid spacing for FFT
> freezegrps = ABC
> freezedim =YYY
> ; Temperature coupling is on
> tcoupl = V-rescale ; modified Berendsen thermostat
> tc-grps = ABC  DDD ; 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 = EnerPres ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel = yes ; assign velocities from Maxwell distribution
> gen_temp = 300 ; temperature for Maxwell distribution
> gen_seed = -1 ; generate a random seed
> --
> *Debashis Sahu*
> *Central Salt and Marine Chemical Research Institute*
> *Bhavnagar, Gujarat*
> *India, 364002.*
> --
> Gromacs 

[gmx-users] umbrella versus constraint in the pulling code

[Dr. Vitaly Chaban]

Could anyone please explain the difference between how "umbrella" and
"constaint" options in the pulling code work. Based on the manual, I
expect that the only difference
is that umbrella used harmonic potential to bind pulled group to the
reference group (point), while "constraint" uses shake algorithm to
rigidly bind the groups. However, the simulations shows that this is
not true. With all other options being the same, umbrella provides
expected pulling, while constraint exhibits rather fluctuations of the
pulled group nearby starting position. What do I miss?

Dr. Vitaly V. Chaban

output from the "constraint" simulation with moving reference point
(i.e. pull_geometry = position)
z-coordinate
 6.38675
 5.97254
 5.88948
 5.86992
 5.72523
 5.59002
 5.84313
 5.83232
 5.88722
 5.83665
 6.00198
 5.96873
 5.57108
 5.35213
 5.47916
 5.46968
 5.40241
 5.41725
 5.4732
 5.45464
 5.61582
 5.66366
 5.8005
 5.9086
 6.10943
 6.11296
 6.21684
 5.95532
 5.89226
 6.00983
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Re: [gmx-users] Charge correction PME

[Dr. Vitaly Chaban]

I might be wrong here, but my expectation is that nowadays you should
not do anything explicitly in this regard. The compensating charge is
automatically applied.


Dr. Vitaly V. Chaban


On Sat, Nov 30, 2013 at 5:14 PM, Benrezkallah Djamila
 wrote:
> Dear gmx_users,
>  My question is about the coulomb LR contribution with PME, I can't access
> to david's original post treating this subject in the mailing list (
> http://www.gromacs.org/pipermail/gmx-users/2002-May/001455.html) if it
> exists, because some links are disabled.If any one can send me the page?
> I'm working on a protein in explicit solvent (water) at different
> concentration of salt (NaCl).I need to calculate coulomb LR energy
> interaction between some residues and Cl-/Na+.
>  My question is :should I turn off the charge correction ( when calculating
> electrostatics for no neutral system),and how to do it? or it has a small
> contribution to the energy, and I have no worry about it.
>
> I hope find answers in your replies.
>
> respectively,
> Djamila Benrezkallah
> University of Oran
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Re: [gmx-users] Umbrella Sampling tutorial

[Dr. Vitaly Chaban]

The output you got indicates that the pulled group came to the
location where it is expected by gromacs to be.

The input looks correct, but gromacs' pull code is with surprise
inside. I would try to pull in opposite direction, i.e. pull_vec1 = -0
0 1. Turning off barostat during pulling also saves nerves.

It must be possible to pull through the whole box, not up to the
middle of Z side.

Dr. Vitaly V. Chaban


On Sun, Dec 1, 2013 at 5:07 PM, Justin Lemkul  wrote:
>
>
> On 12/1/13 10:38 AM, shahab shariati wrote:
>>
>> Dear Justin
>>
>> When I placed drug within the lipid bilayer, after Generating
>> Configurations
>> step, I obtained 501 gro files. When I used distance.pl script for these
>> gro files, my summary_distances.dat file is as follows:
>>
>> 00.2756352
>> 10.2535359
>> 20.2447009
>> 30.3004653
>> 40.2936225
>> 50.1910549
>> 60.2493761
>> 70.2033079
>> 80.1769952
>> 90.2731782
>> 100.2927040
>> 110.3717106
>> 120.3232497
>> .
>> .
>> .
>> .
>> 4850.7589852
>> 4860.6876000
>> 4870.6966222
>> 4880.7487700
>> 4890.7043532
>> 4900.6424745
>> 4910.7194880
>> 4920.6209456
>> 4930.6327312
>> 4940.6861565
>> 4950.5513341
>> 4960.6917742
>> 4970.7074009
>> 4980.7403648
>> 4990.6833771
>> 5000.7035147
>>
>> As can be seen the range of distance is 0.27-0.7, while the dimensions of
>> box is  5.92819   6.43131   7.75764.
>>
>> My supposition was that the range of distance should be 0-3.9 (7.75764/2).
>>
>> You are right. The settings depend on where I place everything.
>> This is my first experience in com pulling. Please guide me to use
>> appropriate Pull code parameters in my case (drug molecules within the
>> lipid bilayer).
>>
>> I used following Pull code parameters:
>>
>> ; Pull code
>> pull= umbrella
>> pull_geometry   = position  ; simple distance increase
>> pull_dim= N N Y
>> pull_start  = yes   ; define initial COM distance > 0
>> pull_ngroups= 1
>> pull_group0 = CHOL_DOPC
>> pull_group1 = drg
>> pull_rate1  = 0.001  ; 0.01 nm per ps = 10 nm per ns
>> pull_k1 = 100  ; kJ mol^-1 nm^-2
>> pull_init1  = 0
>> pull_vec1   = 0 0 1
>>
>> Except Pull code parameters, what things are important?
>>
>
> I have never attempted such a pulling procedure.  Hopefully someone else
> will comment on their experiences.  Do not try to hack the tutorial into
> working for your system; the approaches will be quite different.  The manual
> explains the logic behind the different geometries; you may have to
> experiment a bit to get things to work.
>
> -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] umbrella versus constraint in the pulling code

[Dr. Vitaly Chaban]

Hi Thomas -

I would also expect that it works the same way as before and as
described in the manual. However, thus far I am not very successful.
The main application of the "constraint" option is probably to
automatically get evenly spaced windows during pulling, but I am not
able to achieve this. It is quite mysterious.

Vitaly

Dr. Vitaly V. Chaban


On Mon, Dec 2, 2013 at 10:18 AM, Thomas Schlesier  wrote:
> Hi,
> I never used the pull-code with GMX 4.5.x or 4.6.x,but I would assume that
> it'sthe same as in 4.0.x:
> 'Umbrella': Due to the harmonic potential the force and the distance between
> the two particles will fluctuate.
> 'Constraint': Only the force will fluctuate. The (relative) distance between
> the two particles should either stay constant (if v=0) or increase linearly
> (v.ne.0). But still the position of both groups can fluctuate, but only in
> such a way that the constraint isn't violated.
> Greetings
> Thomas
>
>
> Am 30.11.2013 15:41, schrieb
> gromacs.org_gmx-users-requ...@maillist.sys.kth.se:
>>
>> Could anyone please explain the difference between how "umbrella" and
>> "constaint" options in the pulling code work. Based on the manual, I
>> expect that the only difference
>> is that umbrella used harmonic potential to bind pulled group to the
>> reference group (point), while "constraint" uses shake algorithm to
>> rigidly bind the groups. However, the simulations shows that this is
>> not true. With all other options being the same, umbrella provides
>> expected pulling, while constraint exhibits rather fluctuations of the
>> pulled group nearby starting position. What do I miss?
>>
>> Dr. Vitaly V. Chaban
>>
>> output from the "constraint" simulation with moving reference point
>> (i.e. pull_geometry = position)
>> z-coordinate
>>   6.38675
>>   5.97254
>>   5.88948
>>   5.86992
>>   5.72523
>>   5.59002
>>   5.84313
>>   5.83232
>>   5.88722
>>   5.83665
>>   6.00198
>>   5.96873
>>   5.57108
>>   5.35213
>>   5.47916
>>   5.46968
>>   5.40241
>>   5.41725
>>   5.4732
>>   5.45464
>>   5.61582
>>   5.66366
>>   5.8005
>>   5.9086
>>   6.10943
>>   6.11296
>>   6.21684
>>   5.95532
>>   5.89226
>>   6.00983
>
>
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Re: [gmx-users] using nopbc is not equal to using pbc with big box dimensions

[Dr. Vitaly Chaban]

The fact that images are separated by a distance exceeding the cutoff,
does not mean that they do not interact electrostatically.

I hope the results are not much different...


Dr. Vitaly V. Chaban


>
> On Mon, Dec 2, 2013 at 11:46 PM, Golshan Hejazi 
> wrote:
>
>> Hello,
>>
>> I would like to compute the energy of a system in vacuum. For this I first
>> computed energy by using nopbc and putting rculomb=rvdw=0 ...
>> Then I computed the energy using pbc with a big box dimension (periodic
>> images are separated by a length more than cutoff )... this means that
>> periodic images dont interact ... results are different ... but which one
>> is correct?
>>
>>
>> Can you help me to understand this better
>> G.
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[gmx-users] Fwd: using nopbc is not equal to using pbc with big box dimensions

[Dr. Vitaly Chaban]

So, remove PME in the large box case and everything must be nice.



Dr. Vitaly V. Chaban


On Tue, Dec 3, 2013 at 2:14 AM, Golshan Hejazi  wrote:
> Thanks for your reply. The result is surprisingly different:
>
> with nopbcPotential energy=   -2.53730634908684e+05
> with large boxPotential energy=  -2.21066633251456e+05
>
> I have tried with very large boxes too! but results are not even similar.
> This is what I am using as input in mdp file:
> pbc= no
> nstlist = 0
> epsilon_r= 1.
> ns_type  = Simple
> coulombtype  = Cut-off
> vdwtype = Cut-off
> fourierspacing= 0.12
> ; EWALD/PME/PPPM parameters
> pme_order = 4
> ewald_rtol  = 1e-05
> epsilon_surface  = 0
> optimize_fft= yes
> rlist= 0.
> rcoulomb   = 0.
> rvdw  = 0.
> emtol = 1.0
>
> And this is for when I use the large box:
> pbc   = xyz
> nstlist   = 10
> epsilon_r  = 1.
> ns_type= grid
> coulombtype = pme
> vdwtype  = Cut-off
> fourierspacing   = 0.12
> ; EWALD/PME/PPPM parameters
> pme_order= 4
> ewald_rtol   = 1e-05
> epsilon_surface  = 0
> optimize_fft = yes
> rlist = 0.7
> rcoulomb = 0.7
> rvdw   = 0.7
> emtol = 1.0
>
>
>
> On Monday, December 2, 2013 7:45 PM, Dr. Vitaly Chaban 
> wrote:
> The fact that images are separated by a distance exceeding the cutoff,
> does not mean that they do not interact electrostatically.
>
> I hope the results are not much different...
>
>
> Dr. Vitaly V. Chaban
>
>
>>
>> On Mon, Dec 2, 2013 at 11:46 PM, Golshan Hejazi
>> wrote:
>>
>>> Hello,
>>>
>>> I would like to compute the energy of a system in vacuum. For this I
>>> first
>>> computed energy by using nopbc and putting rculomb=rvdw=0 ...
>>> Then I computed the energy using pbc with a big box dimension (periodic
>>> images are separated by a length more than cutoff )... this means that
>>> periodic images dont interact ... results are different ... but which one
>>> is correct?
>>>
>>>
>>> Can you help me to understand this better
>>> G.
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Re: [gmx-users] Using several cores for MD production

[Dr. Vitaly Chaban]

The invocation line depends on the MPI tool installed on the cluster.

E.g. in case of openmpi, you write
openmpi -np 64 mdrun -dd 4 4 4


Dr. Vitaly V. Chaban


On Tue, Dec 3, 2013 at 4:58 PM, MUSYOKA THOMMAS
 wrote:
> Dear Justin,
> Well it seems i am the first one to do MD simulations in my lab and i am
> using a chemistry department cluster and nobody has prior knowledge on
> GROMACS. I can use all the cores in the cluster but need to know if there
> is a specific mdrun command that can allow me specify the number of cores
> to be used for the MD run.
>
> Thank you
>
>
> On Tue, Dec 3, 2013 at 5:37 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 12/3/13 10:23 AM, MUSYOKA THOMMAS wrote:
>>
>>> Dear Users,
>>>
>>> I am using a cluster of 64 cores to perform my MD simulations using
>>> GROMACS
>>> version 4.5.5.
>>>
>>> I would be glad to know the exact mdrun command that will allow me use the
>>> available resources.
>>>
>>>
>> The answer depends entirely on the architecture of the cluster.  Your sys
>> admin should know.
>>
>> -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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> *MUSYOKA THOMMAS MUTEMIMob nos **+27844846540*
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> (Nagasaki University)*
>
> *PhD Student - Research Unit in Bioinformatics (RUBi - Rhodes 
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>
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>
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>
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Re: [gmx-users] heating

[Dr. Vitaly Chaban]

Honestly, I see no sense in heating from from 0 to 300 K. As long as
the system is in the solid state, it is probably not informative to
handle it. Thus heating, if any, might start from the freezing point.
Moreover, heating from 0 to 300 K over 100 ps is so fulminant that it
does not correspond to any real process...


Dr. Vitaly V. Chaban


On Wed, Dec 4, 2013 at 8:58 AM, rajat desikan  wrote:
> Hi Kiana,
> I always heat from 5 K to 300 K with ref_t=300 (ending temp) and gen_temp=5
> (starting temp). 5 K is as good as starting at 0 K for my systems. Hope
> that helps.
>
> Regards,
>
>
> On Wed, Dec 4, 2013 at 12:18 PM, kiana moghaddam 
> wrote:
>
>> Dear Jastin
>>
>> Thanks very much for your reply, when I heat system from 0 to 300 K with
>> simulated annealing, ref_t =300 is correct?
>>
>> Best Regards
>>
>>
>>
>> On Tuesday, December 3, 2013 5:53 PM, Justin Lemkul 
>> wrote:
>>
>>
>>
>> On 12/3/13 2:17 AM, kiana moghaddam wrote:
>> > Dear GMX Users
>> >
>> > I want to run NVT equilibration and NPT equilibration (after NVT) and
>> want to increase temperature gradually i.e. from 0 to 300 K over 100 ps,
>> but I have some questions about this process:
>> > when I use simulated annealing in NVT as following
>> > annealing_time  =  0  15  30  45   60  80  100
>> > annealing_temp  = 0  50 100 150 200 250 300
>> > I don't know how to change gen_temp. Should gen_temp be 0 or 300 K?
>> >
>>
>> Generating velocities and then immediately freezing (in the strictest of
>> sense)
>> the system is likely not going to be stable or effective because the
>> thermostat
>> will go haywire trying to compensate for such a drastic change in
>> temperature.
>> It is an interesting question, because how does one generate velocities at
>> 0 K?
>>   Theoretically, there are none.  I would suggest setting gen_temp to 0;
>> you can
>> check the .tpr (via gmxdump) to see if any velocities are present, but
>> even if
>> they are they should be very small and largely irrelevant.  The annealing
>> protocol will warm the system relatively quickly, so even after a few
>> dynamics
>> steps, you will have small velocities within the system.
>>
>>
>> > At the first time, I did not use simulated annealing. I prepared 7 mdp
>> files that in the first mdp file, I set nsteps=0, gen_temp=0, ref_t=0, then
>> I use the output from first NVT equilibration for the second input. I
>> repeat this to reach 300 K (in the second step nsteps=7500(*0.002=15),
>> gen_temp=50, ref_t=50). I 'm not sure whether this process is correct?
>>
>> Well, it works, but it's laborious and unnecessary because you're just
>> manually
>> doing what simulated annealing is doing.
>>
>> -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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>
>
>
> --
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> Prof. K. Ganapathy Ayappa's Lab (no 13),
> Dept. of Chemical Engineering,
> Indian Institute of Science, Bangalore
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Re: [gmx-users] rcoulomb, rvdw and rlist values

[Dr. Vitaly Chaban]

the only way to find out, whether it is correct, is to read the paper,
where the force field was derived.


Dr. Vitaly V. Chaban


On Wed, Dec 4, 2013 at 12:17 PM, kiana moghaddam  wrote:
> Dear Users
> I want to use parmbsc0 force field for DNA-ligand interaction. I want some 
> information about value of rcoulomb, rvdw and rlist in mdp file during 
> equilibration & production steps.
> I set these values 1 nm . Is it correct?
>
> Best regards
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Re: [gmx-users] deformation in cnt

[Dr. Vitaly Chaban]

If the system does not explode, everything is correct. Though your
solution is perhaps in the wrong place in relation to the tube.


Dr. Vitaly V. Chaban


On Tue, Dec 10, 2013 at 10:02 AM, Atila Petrosian
 wrote:
> Dear Justin
>
>
> Based on your suggestion, I added C-C bond length to z dimension of box
> (before: 5.5 3.5 3.5, now: 5.5 3.5 3.6418).
>
> Then I used genion to neutralize system using replacing 2 water molecules
> by 2 Na ions, gro file obtained from genion is strange.
>
> When I see this gro file by vmd, some carbon atoms of CNT leave the  box.
>
> Figure is in the bellow link:
>
> https://www.dropbox.com/s/kt1xk4ps3kbxze3/cnt-pic.docx
>
>
> What is reason of this issue?
>
> How to fix it?
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Re: [gmx-users] Parrinello-Rahman barostat: temperature and potential energy depend on tau_p

[Dr. Vitaly Chaban]

I would suggest to repost this in the bug management system.

http://bugzilla.gromacs.org/


Dr. Vitaly V. Chaban


On Tue, Jan 7, 2014 at 12:37 PM, Andrey Frolov  wrote:
> Dear GMX-Users,
>
> Still no reply. I repost the questions. Any suggestions?
>
>
> Andrey Frolov wrote
>>
>> I am simulating pure supercritical CO2 fluid in NPT ensemble. Reference
>> temperature is 308.15K. I use “sd” (Langevin dynamics) to control
>> temperature with tau_t = 2ps. After 100 ps of equilibration  in NPT with
>> Berendsen thermostat, I run production simulation of 10 ns with
>> Parrinello-Rahman barostat. I checked several values of tau_p (from 2 to
>> 100 ps) with the compressibility set to 4.5e-5 bar^-1.
>>
>> 1) Temperature as given in the mdrun log file and edr files is higher than
>> the reference temperature. Moreover, the temperature depends on tau_p: the
>> larger tau_p the lower the resulting T:
>>  tau_p   Quantity  Average
>> Err.Est.RMSD  Tot-Drift
>>2.0Temperature 437.688
>> 6.882.86115.83615  (K)
>>5.0Temperature 321.009
>> 0.4910.13461.51488  (K)
>>   10.0Temperature 314.071
>> 0.187.06755   0.588431  (K)
>>   15.0Temperature 312.508
>> 0.26.48075   0.725419  (K)
>>   20.0Temperature 311.831
>> 0.126.48166 -0.0137431  (K)
>>   25.0Temperature 311.783
>> 0.0936.48474  -0.713862  (K)
>>   30.0Temperature 311.289
>> 0.0996.41436   0.764874  (K)
>>   50.0Temperature 311.392
>> 0.15 6.5612   0.585978  (K)
>>  100.0Temperature 311.278
>> 0.116.51524   0.488872  (K)
>>
>> What could cause such behavior? Could it be that the kinetic energy
>> associated with additional degrees of freedom (motion of the the
>> simulation box edge length) added by Parrinello-Rahman barostat is NOT
>> subtracted from the kinetic energy of the system when the temperature is
>> calculated?
>>
>> 2) Potential energy also depends on tau_p:
>>  tau_p   Quantity  Average
>> Err.Est.RMSD  Tot-Drift
>>2.0   Potential   374.131
>> 120 1535.4 89.344  (kJ/mol)
>>5.0   Potential  -1757.13
>> 11225.17624.8182  (kJ/mol)
>>   10.0   Potential  -1879.24
>> 4.6 186.865.23366  (kJ/mol)
>>   15.0   Potential  -1912.12
>> 5.3183.54225.0223  (kJ/mol)
>>   20.0   Potential  -1927.11
>> 4.1198.066   -9.76647  (kJ/mol)
>>   25.0   Potential  -1922.43
>> 7187.913   -22.8972  (kJ/mol)
>>   30.0   Potential  -1939.59
>> 5.9175.81332.3813  (kJ/mol)
>>   50.0   Potential  -1935.01
>> 8.4  182.911.7818  (kJ/mol)
>>  100.0   Potential  -1930.76
>> 8.3  199.640.4494  (kJ/mol)
>>
>> I would appreciate if someone can explain the dependence of potential
>> energy on “tau_p”.
>> Could it be explained by the implementation problem of Parinello-Rahman
>> with leap-frog algorithm discussed in the manual:  “... using the
>> leap-frog algorithm, the pressure at time t is not available until after
>> the time step has completed, and so the pressure from the previous step
>> must be used, which makes the [Parrinello-Rahman] algorithm not directly
>> reversible, and may not be appropriate for high precision thermodynamic
>> calculations.”?
>>
>> Densities and pressures are identical among these simulations. As I can
>> see from the density VS time plots the period of density oscillations
>> corresponds roughly to 4*tau_p.
>>
>> Also, it seems that the potential energy goes to plateau when tau_p > 20
>> ps. Does it show that for my system I should not use tau_p less than 20 ps
>> at given compressibility value and that with tau_p > 20 ps the true NPT
>> ensemble is sampled?
>>
>> Thank you very much.
>> Andrey
>
>
>
> -
> 
> Andrey I. Frolov, PhD
> Junior researcher
> Institute of Solution Chemistry
> Russian Academy of Sciences
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Re: [gmx-users] Simulations in extreme conditions

[Dr. Vitaly Chaban]

I like extreme conditions... Seriously.

OPLS water, as well as other popular MM waters, are parametrized for
liquid state. I think you need to decrease model's dipole moment and
you have to work with an integration time-step to ensure adequate
energy conservation at ca. 600K.

I believe there should be exotic water models that were trained to
reproduce the phase diagram to certain extent.

Vitaly



On Fri, Feb 14, 2014 at 7:58 PM, CipPruteanu  wrote:
> Hi everyone!
>
> I am trying to run a simulation of methane-water mixtures under extreme
> conditions, that is around 25 kbars and 600K (and maybe higher in both
> pressure and temperature).
>
> I am currently using OPLS for methane with TIP3P for water. The way I
> proceed is as follows:
>
> -generate a box of methane and water having my desired concentration
> -do an energy minimization for 100ps
> -do a NVT equilibration at my desired temperature for 100ps
> -do a NPT equilibration at my desired pressure and temperature for 100ps
>
> -run the simulation (NPT) for as long as I desire (1-10 ns for the moment)
>
> The simulations I ran on the individual components get reasonably good
> results for them under these conditions. However, once I put them together,
> the mixture doesn't behave as expected (by recent experimental findings).
>
> Is this approach ok or is there something fundamentally flawed about it ? I
> know the fact that the forcefields are not meant to be used at these high
> pressures/temperatures, but apart from that, is there anything I could
> improve?
>
> --
> View this message in context: 
> http://gromacs.5086.x6.nabble.com/Simulations-in-extreme-conditions-tp5014553.html
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Re: [gmx-users] Simulations in extreme conditions

[Dr. Vitaly Chaban]

>> I am aware of the fact that GROMACS "doesn't really like" crystal structure,
>> but this is generally fine with me since I run my simulations in a region
>> which is experimentally know to be liquid state (both the water and
>> methane). I am aware t hat it works best with liquids, and that is very well
>> since it is exactly the liquid phases of the mixture  that I'm interested
>> in.
>
>
> At 600K and under 25kbar ... water&methane mixture ... liquid state
>  H. Did you point out incorrect pressure?


Sorry, my fault. I read "bar" as "Pa". The system should be liquid
then. This does not change other considerations, though.



Dr. Vitaly V. Chaban
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