[gmx-users] Regarding combination rules in gromos53a6 ff

[Apramita Chand]

Dear GROMACS users,
 I want to use the geometric mean of both sigma (sigma i sigmaj)and
epsilon(epsilon i epsilon j) as a combination rule in my simulation.
According to the combination rules in the manual, the combination 3
incorporates Vii=sigma and Wii= epsilon along with geometric mean of Ci(6)
Cj(6) and Ci(12)Cj(12) terms.
So can I use combination 3 in the [defaults] section of the forcefield.itp ?
If not, how do I achieve this particular combination?

Thanking you,
Yours sincerely,
Apramita
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[gmx-users] source code for velocity information

[刘杰]

Dear all, Iam trying to add viscidity bond code to gromacsc 4.0.7. I  found the 
harmonic bond code in bondfree.c ,but i could not conform which source document 
include the velocity information . Can somebody please advise me on how to 
overcome this issue?Thank you. Regards, jieliu
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[gmx-users] source code for velocity information

[刘杰]

Dear all, Iam trying to add viscidity bond code to gromacsc 4.0.7. I  found the 
harmonic bond code in bondfree.c ,but i could not conform which source document 
include the velocity information . Can somebody please advise me on how to 
overcome this issue?Thank you. Regards, jieliu




 
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Re: [gmx-users] Potential energy

[Justin Lemkul]

On 3/20/18 7:15 PM, Alex wrote:

Thanks Justin.

On Tue, Mar 20, 2018 at 3:02 PM, Justin Lemkul  wrote:



On 3/20/18 2:40 PM, Alex wrote:


Dear all,

The potential energy of my system after two minimization steps (with and
without constrained) is converging well, however, it is still positive
around 1000 kj/mol !
I think it is not a good sign for my system, but, what could be the reason
and how I can overcome the issue? The system generated via "gmx
insert-molecules" contains 1000 molecules of "C21H28O4".


Look at the individual values of internal (bonded) terms and nonbonded
terms. Likely the intermolecular interactions are fairly weak, and the
potential energy of the system is dominated by internal terms, which are by
definition positive.


I changed the minimization criteria, now I have a negative potential energy
around (-332 kj/mo), and below are the list of different energies: the
bond, angle and LJ/Coulomb-14 are positive. Do you think having a weak
intermolecular interactions is a problem for the system?
Energy  Average   Err.Est.   RMSD  Tot-Drift

---
Bond819.2869.2 27.407   -42.6564
(kJ/mol)
Angle   1948.894.49.80344-23.362
(kJ/mol)
Proper Dih. 252.261  0.011  0.0262872  0.0474904
(kJ/mol)
LJ-14   8356.141.2 2.4604   -7.05906
(kJ/mol)
Coulomb-14  5798.87   0.19   0.357136   -1.13575
(kJ/mol)
LJ (SR)-9800.04   0.11   0.219992  -0.772991
(kJ/mol)
Disper. corr.  -423.936  0  0  0
(kJ/mol)
Coulomb (SR)   -9722.23   0.15   0.284124   0.915601
(kJ/mol)
Coul. recip.267.995 0.0039  0.0126721  0.0266248
(kJ/mol)
Potential  -332.748 1539.6655   -75.3192
(kJ/mol)
Pres. DC  0  0  0  0  (bar)


I don't see any problems here.

-Justin



Regards,
Alex


Second question;

To calculate the RDF between pair of atoms, let's say A and B, I was
wondering if those two atoms should be differentiated in index.ndx file
from beginning before invoking the gmx gromps?(similar to energygrps) or
one can does the simulation without index.ndx and still possible to
calculate the RDF between those two atoms?


There is no need for anything like energygrps. If you want to exclude the
intramolecular contribution to the RDF (if relevant), you have to increase
nrexcl in the topology and generate a new .tpr, otherwise everything is
controlled by index groups.

-Justin

--
==

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

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

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

==

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Assistant Professor
Virginia Tech Department of Biochemistry

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

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

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Re: [gmx-users] Potential energy

[Alex]

Thanks Justin.

On Tue, Mar 20, 2018 at 3:02 PM, Justin Lemkul  wrote:

>
>
> On 3/20/18 2:40 PM, Alex wrote:
>
>> Dear all,
>>
>> The potential energy of my system after two minimization steps (with and
>> without constrained) is converging well, however, it is still positive
>> around 1000 kj/mol !
>> I think it is not a good sign for my system, but, what could be the reason
>> and how I can overcome the issue? The system generated via "gmx
>> insert-molecules" contains 1000 molecules of "C21H28O4".
>>
>
> Look at the individual values of internal (bonded) terms and nonbonded
> terms. Likely the intermolecular interactions are fairly weak, and the
> potential energy of the system is dominated by internal terms, which are by
> definition positive.
>
I changed the minimization criteria, now I have a negative potential energy
around (-332 kj/mo), and below are the list of different energies: the
bond, angle and LJ/Coulomb-14 are positive. Do you think having a weak
intermolecular interactions is a problem for the system?
Energy  Average   Err.Est.   RMSD  Tot-Drift

---
Bond819.2869.2 27.407   -42.6564
(kJ/mol)
Angle   1948.894.49.80344-23.362
(kJ/mol)
Proper Dih. 252.261  0.011  0.0262872  0.0474904
(kJ/mol)
LJ-14   8356.141.2 2.4604   -7.05906
(kJ/mol)
Coulomb-14  5798.87   0.19   0.357136   -1.13575
(kJ/mol)
LJ (SR)-9800.04   0.11   0.219992  -0.772991
(kJ/mol)
Disper. corr.  -423.936  0  0  0
(kJ/mol)
Coulomb (SR)   -9722.23   0.15   0.284124   0.915601
(kJ/mol)
Coul. recip.267.995 0.0039  0.0126721  0.0266248
(kJ/mol)
Potential  -332.748 1539.6655   -75.3192
(kJ/mol)
Pres. DC  0  0  0  0  (bar)


Regards,
Alex

>
> Second question;
>> To calculate the RDF between pair of atoms, let's say A and B, I was
>> wondering if those two atoms should be differentiated in index.ndx file
>> from beginning before invoking the gmx gromps?(similar to energygrps) or
>> one can does the simulation without index.ndx and still possible to
>> calculate the RDF between those two atoms?
>>
>
> There is no need for anything like energygrps. If you want to exclude the
> intramolecular contribution to the RDF (if relevant), you have to increase
> nrexcl in the topology and generate a new .tpr, otherwise everything is
> controlled by index groups.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
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Re: [gmx-users] Topol file for a bigger system

[Justin Lemkul]

On 3/20/18 6:06 PM, Alex wrote:

On Mon, Mar 19, 2018 at 8:57 PM, Justin Lemkul  wrote:



On 3/19/18 8:15 PM, Alex wrote:


Dear all,

Using topolbuild I can generate the case.gro, case.top, ffcase.itp and
posrecase.itp out of a case.mol2 which contain only a single molecule of
X.

Also, using the "gmx insert-molecules" I can generate a bigger system
containing 1000 molecule of X, for example to have case-1000.gro.

Now, I was wondering how I can update the case.top and itp files for the
new system? I am trying the "gmx x2top" but first of all it is really time
consuming and also at the end it can not find the force fields for some of
the atoms.
(~> gmx x2top -f case-1000.gro -o out.top -r out.rtp)


Shouldn't it be as simple as updating the number of molecules in the .top
file to 1000?


You are right. Thank you.


There are no changes in .itp files, as only a .top keeps record of how
many of each species there are.


How about the posre.itp (the position restrain file)? The initial posre.itp
only have the restrain only on the atoms of X molecule, whereas I might
need to update it when the system has 1000X molecules.


This file requires no change. Position restraints are applied on a 
per-moleculetype level, so changes in global atom number are irrelevant.



One more question:
The gmx grompp in gromacs 2018, needs to have the positions of the atom for
which restrain has been defined in posre.itp file to be read in "gmx grompp
-f .. *-c conf.gro* *-r restraint.gro* .. ", am I right? then, should we
update the restraint.gro file according to the conf.gro file? I means
between each level of simulation (equalization, production .) where gmx
grompp is invoked we have to give a new restraint.gro file each time?


Yes.

-Justin

--
==

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

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

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

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Re: [gmx-users] Topol file for a bigger system

[Alex]

On Mon, Mar 19, 2018 at 8:57 PM, Justin Lemkul  wrote:

>
>
> On 3/19/18 8:15 PM, Alex wrote:
>
>> Dear all,
>>
>> Using topolbuild I can generate the case.gro, case.top, ffcase.itp and
>> posrecase.itp out of a case.mol2 which contain only a single molecule of
>> X.
>>
>> Also, using the "gmx insert-molecules" I can generate a bigger system
>> containing 1000 molecule of X, for example to have case-1000.gro.
>>
>> Now, I was wondering how I can update the case.top and itp files for the
>> new system? I am trying the "gmx x2top" but first of all it is really time
>> consuming and also at the end it can not find the force fields for some of
>> the atoms.
>> (~> gmx x2top -f case-1000.gro -o out.top -r out.rtp)
>>
>
> Shouldn't it be as simple as updating the number of molecules in the .top
> file to 1000?
>
You are right. Thank you.

>
> There are no changes in .itp files, as only a .top keeps record of how
> many of each species there are.
>

How about the posre.itp (the position restrain file)? The initial posre.itp
only have the restrain only on the atoms of X molecule, whereas I might
need to update it when the system has 1000X molecules.

One more question:
The gmx grompp in gromacs 2018, needs to have the positions of the atom for
which restrain has been defined in posre.itp file to be read in "gmx grompp
-f .. *-c conf.gro* *-r restraint.gro* .. ", am I right? then, should we
update the restraint.gro file according to the conf.gro file? I means
between each level of simulation (equalization, production .) where gmx
grompp is invoked we have to give a new restraint.gro file each time?

Regards,
Alex


>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
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Re: [gmx-users] nve energy conservation

[Jo]

Thanks everyone for your reply.
I see your point that it could just be some error cancellation from
constraints and parameters.

I was previously using gromacs-5.1.4, and changed to gromacs-2018, and the
drift seems to be much smaller! I get something similar to what Mark had
posted -0.25 kJ/mol/ps/atom for 1000 SPCE waters with settles at 298K
for single precision.  With double precision, there is no noticeable drift
for a short test run of only 200 ps. Any idea why this is? Is there some
default setting that changed?

Mark, regarding your earlier questions: My application is to calculate very
precise and accurate dynamic properties (diffusion, viscosity) of NaCl in
water. There are a number of works in literature where people use NVT
simulations to calculate these properties, but I wanted to check if the
thermostat affected the dynamics any by running an NVE simulation.  Also I
want to better understand how NVE simulations work and all the controlling
factors.

>From figure 3.5 in the reference manual, I think 10^-5 drift (kJ/mol/ps) is
acceptable.

Can you help me better understand what verlet-buffer-tolerance does?  My
understanding from the documentation is that it determines the width of the
buffer outside of the cutoff for the neighborlist, but I am not clear why
energy can be added or lost by manipulating this parameter.

Also, I am not sure how to judge what is an acceptable width of fluctuation
NVE simulations?  Does it correspond to random error (from the paper
Mark
referenced)?

Thank you!











On Tue, Mar 20, 2018 at 1:39 AM, Mark Abraham 
wrote:

> Hi,
>
> On Mon, Mar 19, 2018 at 10:08 PM Jo  wrote:
>
> > Hello,
> >
> > Thank you for your response.  I have found a way to conserve energy of my
> > box of SPC/E water by removing 'settles' from my topology file.
> >
>
> Thus your water is no longer rigid.
>
>
> > Previously, the total energy of the system was consistently increasing or
> > decreasing by a significant amount resulting in no energy conservation.
> >
>
> You're doing a numerical computation with finite-precision forces,
> positions and velocities and a discrete fixed time step. You are guaranteed
> to have both random and systematic errors compared to exact arithmetic.
> Maybe you can find a parameter combination that will appear to lack
> systematic errors, but that doesn't mean errors are absent, or the
> combination is "better," as you have no doubt already read about in the
> article I shared.
>
>
> > I have defined 'bonds' and 'angles' with length and force constant for a
> > flexible SPC/E water, with no 'settles' and no 'constraints'.  For these
> > parameters, the total energy converges to approximately the correct
> energy
> > and fluctuates withing 40 kJ/mol for a timestep of 1 fs, which is good.
> >
>
> Why is it good? :-)
>
>
> > However, I don't understand why or how removing the constraints allowed
> for
> > energy conservation.
>
>
> It is implementing different equations of motion. If the only observable of
> interest is the potential energy, and the multiple sources of numerical
> inaccuracy are cancelling suitable for you, and you can afford to generate
> enough samples at that short time step, then go right ahead :-)
>
>
> > Does simply defining 'bonds' and 'angles' actually
> > force the atoms to to constrained as a rigid molecule.
>
>
> No, see the documentation about bonded interactions...
>
>
> >   If not, why does
> > adding some sort of constraint make the system loose energy conservation?
> >
>
> It is implementing different equations of motion, and they have different
> numerical properties. Whether those properties are sufficient for any
> purpose is an open question. I note that you ignored my earlier series of
> questions on this topic, which were intended to help you learn ;-)
>
> How can I go about constraining the atoms as a rigid water molecule so that
> > I don't loose energy conservation?
> >
>
> As you can infer from Figure 3.5 in the reference manual, you can choose
> the drift from the verlet buffer to add enough energy to offset the drift
> from SETTLE. But obviously that would be a pair of compensating systematic
> errors - so you won't learn anything from merely observing
> that the systematic drift is zero.
>
> Mark
>
>
> > Thank you in advance,
> >
> > Jo
> >
> > On Fri, Mar 16, 2018 at 4:51 PM, Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > On Fri, Mar 16, 2018 at 7:42 PM Jo  wrote:
> > >
> > > > Thank you for your reply!
> > > >
> > > > I am attempting to conserve energy in an NVE run of 1000 SPCE water
> - I
> > > > have tried a number of different verlet-buffer-tolerances (0.001 to
> > > 5e-5),
> > > > sometimes the run output file suggests a specific verlet
> > > buffer-tolerance.
> > > > However I am still experiencing ~600 kJ/mol shift per ns.
> > >

[gmx-users] Regarding time steps for calculation of Hydrogen Bond Dynamics

[Dilip H N]

Hello all,

I have run a simulation for 10 ns (0.001 * 1000 = 1 ps) and have
saved the data for every 0.5 ps (nstxout= 500etc.,...) (which comes to
2 frames...).
Since if i extract the trajectory in .gro format for the full simulation,it
will be such a huge file, so i intended to extract the trajectories having
500 frames since it will be relatively less file size. The command is:

gmx trjconv -f nptmd.xtc -s nptmd.tpr -pbc mol -o nptmdtrj500.gro -dt 20

which gives the full trajectory, but has 500 frames in total (ie., from
t=0ns to t=10ns, the frames are 500 with an interval of 20 ns).

So, my question is that, is this trajectory sufficient/good to analyze the
hydrogen bond dynamics (intermittent and continuous)...??
I have the trajectories extracted in .gro file for time t=0, t=20, t=40 and
so on... So the interactions/bonding is taken for t=20 ns... Is this affect
the dynamics study..??

Can anybody suggest the best possible way of trajectories (like how many
time frames/intervals etc.,) to be taken for HB Dynamics..??

Any suggestions are highly appreciated.

Thank you.
-- 
With Best Regards,

DILIP.H.N
PhD Student



‌
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Re: [gmx-users] Potential energy

[Justin Lemkul]

On 3/20/18 2:40 PM, Alex wrote:

Dear all,

The potential energy of my system after two minimization steps (with and
without constrained) is converging well, however, it is still positive
around 1000 kj/mol !
I think it is not a good sign for my system, but, what could be the reason
and how I can overcome the issue? The system generated via "gmx
insert-molecules" contains 1000 molecules of "C21H28O4".


Look at the individual values of internal (bonded) terms and nonbonded 
terms. Likely the intermolecular interactions are fairly weak, and the 
potential energy of the system is dominated by internal terms, which are 
by definition positive.



Second question;
To calculate the RDF between pair of atoms, let's say A and B, I was
wondering if those two atoms should be differentiated in index.ndx file
from beginning before invoking the gmx gromps?(similar to energygrps) or
one can does the simulation without index.ndx and still possible to
calculate the RDF between those two atoms?


There is no need for anything like energygrps. If you want to exclude 
the intramolecular contribution to the RDF (if relevant), you have to 
increase nrexcl in the topology and generate a new .tpr, otherwise 
everything is controlled by index groups.


-Justin

--
==

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

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

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

==

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[gmx-users] Potential energy

[Alex]

Dear all,

The potential energy of my system after two minimization steps (with and
without constrained) is converging well, however, it is still positive
around 1000 kj/mol !
I think it is not a good sign for my system, but, what could be the reason
and how I can overcome the issue? The system generated via "gmx
insert-molecules" contains 1000 molecules of "C21H28O4".

Second question;
To calculate the RDF between pair of atoms, let's say A and B, I was
wondering if those two atoms should be differentiated in index.ndx file
from beginning before invoking the gmx gromps?(similar to energygrps) or
one can does the simulation without index.ndx and still possible to
calculate the RDF between those two atoms?

Thank you.

Regards,
Alex
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Re: [gmx-users] crystal lattice topology generation

[Alex]

Prior to generating the topology (say, with x2top) use editconf on your 
coordinates to put the crystal in a box of size that's compatible with 
the periodicity and the number of unit cells in your crystal sample.


Alex

On 3/20/2018 10:49 AM, Bala subramanian wrote:

Dear Grom. users,

Greetings,

I have to simulate a crystal lattice with gromacs. In the unit cell, there
are 16 copies of the mineral (Lets say 16 residues). If all residues have
the same number of atoms, I can simply create the .rtp file for one residue
and then proceed for the topology generation.

In my lattice, residues at one edge, for instance, interact those in the
other side of the crystal due to periodicity. Hence, I am stuck not knowing
the apt strategy to create the topology. Any insights to deal with this
issue based on your experience could be of much help to me.

Thanks,

Bala




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[gmx-users] crystal lattice topology generation

[Bala subramanian]

Dear Grom. users,

Greetings,

I have to simulate a crystal lattice with gromacs. In the unit cell, there
are 16 copies of the mineral (Lets say 16 residues). If all residues have
the same number of atoms, I can simply create the .rtp file for one residue
and then proceed for the topology generation.

In my lattice, residues at one edge, for instance, interact those in the
other side of the crystal due to periodicity. Hence, I am stuck not knowing
the apt strategy to create the topology. Any insights to deal with this
issue based on your experience could be of much help to me.

Thanks,

Bala


-- 
C. Balasubramanian
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[gmx-users] Regarding combination rules in gromos53a6 ff

[Apramita Chand]

Dear GROMACS users,
 I want to use the geometric mean of both sigma (sigma i sigmaj)and
epsilon(epsilon i epsilon j) as a combination rule in my simulation.
According to the combination rules in the manual, the combination 3
incorporates Vii=sigma and Wii= epsilon along with geometric mean of Ci(6)
Cj(6) and Ci(12)Cj(12) terms.
So can I use combination 3 in the [defaults] section of the forcefield.itp ?
If not, how do I achieve this particular combination?

Thanking you,
Yours sincerely,
Apramita
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Re: [gmx-users] Free Energy solvation generate multiple dhdl.xvg output files

[Javier Luque Di Salvo]

Dear Wes,

Thanks for clarifying, I did as you told and it worked. The resulting
dG_hyd of NH4+ is -62.5 kJ/mol, while the experimental value is -285 kJ/mol
(10.1039/FT9918702995). I am using OPLS and SPC/E water. Energy values of
the last lambdas showed higher error bars, so now I am refining the last
part by increasing the number of lambda points:
fep-lambdas  = 0.0 0.2 0.4 0.6 0.8 0.85 0.9 0.92 0.94 0.96 0.98
1.0
I do not expect big differences. I could also try (i) other water model,
(ii) bigger box with more NH4+ ions (same concentration) or (ii-b) increase
NH4+ concentration, (iii) adding anions (like Cl-). Regarding these
options, I am not sure yet if they have sense (meaning that there may be
another more suitable option, while some of the possible tests I wrote may
not result in significative improvements), so if there are any comments
regarding these options they are welcome.

Also, I do not understand why the Nitrogen partial charge is negative,
shouldnt be positive? I choose OPLS since it was parameterized for liquid
simulations, but I found in literature that usually there are problems for
correctly simulating dG_hyd of amines.
 atom charge   mass
 N00-0.518314.0070
 H01 0.3796 1.0080
 H02 0.3796 1.0080
 H03 0.3796 1.0080
 H04 0.3796 1.0080
Maybe the best option is to change FF (does someone know about an
acceptable FF -preferably all_atoms- for amines/ ammonium derivatives R4N+)
?

Best regards
Javier

Date: Mon, 19 Mar 2018 13:50:19 -0400
> From: Wes Barnett 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Free Energy solvation generate multiple
> dhdl.xvg output files
> Message-ID:
> 

Re: [gmx-users] Separate structure from box

[Wes Barnett]

On Tue, Mar 20, 2018 at 2:30 AM, rose rahmani  wrote:

> Hi,
> I want to extract a structure in a box, i mean i want to extract a sheet
> from the box of solution, because i dont have any separated .gro file from
> my sheet. How can i do that?
>

Try creating an index file using "gmx make_ndx" to create an index group
containing just the atoms you want. Then use "gmx trjconv" to output a file
only containing that group. See the "-h" flag for both of those commands.


-- 
James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering
Kumar Research Group 
Columbia University
w.barn...@columbia.edu
http://wbarnett.us
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Re: [gmx-users] error in grompp step

[Upendra N]

Dear Mark sir,
Thank you... I will try with the later versions.
I am actually using modified version of gromacs-4.6.2[by J S Hub et al.,] ,
for calculating swaxs(small and wide angle x ray scattering) profiles and
swaxs driven MD.
I will learn to incorporate swaxs driven MD to later versions with your
directions and support.

With Regards
Upendra N
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[gmx-users] Free energy of VDW transformation from state A to State B

[deepak bapat]

Dear gmx-users

I am trying to calculate free energy of VDW transformation. The system is
very simple as I want to test the methodology. Single neutral LJ particle
is transformed from state A to state B in TIP4P water.

I have tried simulations with different state B LJ parameters without
changing state A LJ parameters.

I find that at init_lambda = 0.0 dhbydl values are dependent on state B
parameters. And these values vary considerably depending on state B
parameters.

e.g.

1) transformation 1: (TIP4P OW like LJ)

9e-02 & 6.50194e-02TO  3.15365e-01 & 6.48520e-01 : 
= 5061 +- 95 kJ/mol

2) transformation 2: (Neon like LJ)

9e-02 & 6.50194e-02TO  2.78000e-01 & 2.88696e-01 : 
= 1632 +- 30 kJ/mol

3) transformation 3: (All atom methane like LJ)

9e-02 & 6.50194e-02  TO 3.73000e-01 & 1.23010e+00 :  =
19062 +- 417 kJ/mol

Is this behavior normal if initial state is similar in all three
simulations at init_lambda = 0.0

Shouldn't results be equivalent irrespective state B LJ parameters ? Or am
I doing something wrong?

topology file reads something like this


;begin top file

#include "forcefield.itp"

#include "nonbonded.itp"

#include "tip4p.itp"

#include "TPI.itp"

[ system ]

TPI in water

[ molecules ]

SOL 907

TPI 1

; end of top file


I have forcefield.itp, nonbonded.itp, tip4p.itp and TPI.itp in my working
folder.

TPI.itp is as follows


;begin TPI file

[ moleculetype ]

; molname nrexcl

TPI 1

[ atoms ]

; id at type res nr residu name at name cg nr charge mass

1 opls_test 1 TPI OW 2 0.0 20.17970 opls_test_transform 0.0 20.17970

; end TPI file


and nonbonded.itp is shown below


;begin nonbonded

[ atomtypes ]

; TPI

opls_test OW 10 20.17970 0.000 A 9e-02 6.50194e-02 ; state A

opls_test_transform OW 10 20.17970 0.000 A 3.73000e-01 1.23010e+00 ;
transformed to state B

;TIP4P

opls_113 OW 8 15.99940 0.000 A 3.15365e-01 6.48520e-01

opls_114 HW 1 1.00800 0.520 A 0.0e+00 0.0e+00

opls_115 MW 0 0.0 -1.040 D 0.0e+00 0.0e+00

;end nonbonded


some relevant parameters in md.mdp file are

;begin mdp

integrator = md

tinit = 0

dt = 0.001

nsteps = 100

nstcomm = 100

nstxout = 0

nstvout = 00

nstfout = 0

nstlog = 5000

nstenergy = 5000

nstxtcout = 5000

cutoff-scheme = verlet

nstlist = 10

ns_type = grid

pbc = xyz

rlist = 1.0

coulombtype = PME

rcoulomb = 1.0

vdwtype = cutoff

rvdw = 1.0

DispCorr = EnerPres

fourierspacing = 0.12

pme_order = 6

epsilon_surface = 0

tc_grps = system

tcoupl = nose-hoover

tau_t = 0.5

ref_t = 300

Pcoupl = Parrinello-Rahman

tau_p = 1.0

compressibility = 4.5e-05

ref_p = 1.0

; Free energy variables

free_energy = yes

couple-moltype =

couple-lambda0 = vdw-q

couple-lambda1 = vdw-q

couple-intramol = no

init_lambda = 0.0

delta_lambda = 0

nstdhdl = 10

dhdl-print-energy = no

sc-alpha = 0

sc-power = 1

sc-r-power = 6

sc-sigma = 0.3

sc-coul = no

separate-dhdl-file = yes

dhdl-derivatives = yes

dh_hist_size = 0

dh_hist_spacing = 0.1

; end mdp file


Regards

-- 
Deepak
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[gmx-users] Separate structure from box

[rose rahmani]

Hi,
I want to extract a structure in a box, i mean i want to extract a sheet
from the box of solution, because i dont have any separated .gro file from
my sheet. How can i do that?
Thank you
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