[gmx-users] simulation single molecule in water

[Souilem Safa]

Dear gromacs users,
I'm simulating a single molecule in spc water. I'm using a cubic water box
which has 3.4 nm size.
I got the toplogy of my molecule via PRODRG.
After running minimization, NVT , NPT and MD for 10 ns , I checked the
density of water ,it was less than the real value (1000 kg m\S-3\N)
,actually I got around 950.
I have checked my mdp file in the NPT step and I was wondering about tau_p
that I should use. First I used 2.0 ps with Parrinello-Rahman coupling.
After checking in gromacs archive, I found it is better to use 0.5 ps, I
have changed tau-p ,but I still have density value less than 1000.
Details of my  mdp file are below :
 Run parameters
integrator= md; leap-frog integrator
nsteps= 500; 2 * 500 = 1 ps, 1 ns
dt= 0.002; 2 fs
; Output control
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= system; two coupling groups - more accurate
tau_t= 0.1; time constant, in ps
ref_t= 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= 0.50; 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

What should be the origin of this density difference?
looking forward to your advise
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[gmx-users] center of mass and box co-ordinates

[Arunima Shilpi]

Hello Justin sir

In your tutorial file for umbrella sampling for Aβ42 protofibril, what was
the criteria used to determine the coordinates of center of mass and box
size which you have takes as

editconf -f complex.gro -o newbox.gro -center 3.280 2.181 2.4775 -box
6.560 4.362 12



-- 

Thanking You with Regards.

Arunima Shilpi

Ph. D Research Scholar(Cancer & Epigenetics)
Department of Life Science
National Institute of Technology
Rourkela
Odisha
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Re: [gmx-users] keeping water (entirely) out of the bilayer core

[Jianguo Li]

Hi Chris, 


Just think of another possible way without modifying the code. The task can be 
achieved by increasing the LJ repulsion term between the lipid tail atoms and 
water molecules, but keeping all other interactions unchanged. To do so, the 
free energy code can be used. You can create a state_B, at which only the LJ 
repulsion term between the lipid tail atoms and water molecules is rescaled, 
other interactions are the same as state_A, and then run the simulations at 
lambda=1. 

Jianguo




 From: Christopher Neale 
To: "gmx-users@gromacs.org"  
Sent: Monday, 6 May 2013, 2:46
Subject: [gmx-users] keeping water (entirely) out of the bilayer core
 

Thank you for the advice Jianguo. This seems like a good way forward. I was 
hoping not to have to learn how to use new software, but perhaps it is time.

Thank you,
Chris.


-- original message --

Hi Chris,

Perhaps you can try PLUMED+GROMACS. In that case, you can define a collective 
variable as 
mindist between the water molecules and the lipid tails. And then apply wall 
potential to keep 
this CV above a certain value. 

Jianguo 



Dear users:

I am interested in running simulations of lipid bilayers in which I keep all 
water molecules out of
the bilayer core(not just statistically, but absolutely). However, I have been 
unable to figure out
how to do it. I'll list what I have tried in the hope that others have some 
ideas or even perhaps 
know how to do this with standard gromacs.
...
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[gmx-users] mdrun-gpu error message on Gromacs 4.5.5

[Andrew DeYoung]

Hi,

I am running mdrun-gpu on Gromacs 4.5.5 (with OpenMM).  This is my first
time using a GPU.  I get the following error message when attempting to run
mdrun-gpu with my .tpr file: 

---
Program mdrun-gpu, VERSION 4.5.5
Source code file:
/usr/local/src/gromacs-4.5.5/src/kernel/openmm_wrapper.cpp, line: 1365

Fatal error:
OpenMM exception caught while initializating: getPropertyValue: Illegal
property name
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

I get this error when calling with:

mdrun-gpu -s topol.tpr

and with:

mdrun-gpu -device
"OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=no" -s topol.tpr

I can't seem to find this particular error message in the documentation or
previously discussed on this mailing list.  Does this error message suggest
that I am calling mdrun-gpu incorrectly, or that OpenMM is improperly
installed?

Thank you kindly for your time! 

Andrew DeYoung
Carnegie Mellon University

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[gmx-users] RE: keeping water (entirely) out of the bilayer core

[Dallas Warren]

Chris, not entirely sure if would work, but what about set of particles located 
at the center of the bilayer (might require anchoring/freezing) which only 
interacts (via repulsion only) with water, and setting the interaction such 
that it manages to exclude it from the bilayer region you require.

Catch ya,

Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a 
nail. 

> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of Christopher Neale
> Sent: Saturday, 4 May 2013 10:46 AM
> To: gmx-users@gromacs.org
> Subject: [gmx-users] keeping water (entirely) out of the bilayer core
> 
> Dear users:
> 
> I am interested in running simulations of lipid bilayers in which I
> keep all water molecules out of the bilayer core
> (not just statistically, but absolutely). However, I have been unable
> to figure out how to do it.
> I'll list what I have tried in the hope that others have some ideas or
> even perhaps know how to do this
> with standard gromacs.
> 
> Everything that I have tried revolves around using the pull code,
> setting the entire lipid bilayer as the reference
> group, and having thousands of pulled groups -- one for each water
> molecule. Also, I modified the gromacs
> source code in mdlib/pull.c (version 4.6.1) so that the force is only
> applied when the displacement is smaller than
> the desired distance and not when the displacement is larger than the
> specified distance (to keep water out but
> then to otherwise let it go anywhere without bias):
> 
> static void do_pull_pot(int ePull,
> t_pull *pull, t_pbc *pbc, double t, real
> lambda,
> real *V, tensor vir, real *dVdl)
> {
> intg, j, m;
> dvec   dev;
> double ndr, invdr;
> real   k, dkdl;
> t_pullgrp *pgrp;
> 
> /* loop over the groups that are being pulled */
> *V= 0;
> *dVdl = 0;
> for (g = 1; g < 1+pull->ngrp; g++)
> {
> pgrp = &pull->grp[g];
> get_pullgrp_distance(pull, pbc, g, t, pgrp->dr, dev);
> 
> /*  ## HERE IS THE CODE CHANGE 
> if(dev[0]>0.0){
> dev[0]=0.0;
> }
> /* End code snippit */
> 
> 
> The most relevant lines from the .mdp file were:
> 
> pull = umbrella
> pull_geometry= distance
> pull_dim = N N Y
> pull_start   = no
> pull_ngroups = 9000
> pull_group0  = POPC
> 
> pull_group1  = r_1_&_OW
> pull_init1   = 1.9
> pull_k1  = 500
> 
> pull_group2  = r_2_&_OW
> pull_init2   = 1.9
> pull_k2  = 500
> 
> ... etc...
> 
> 
> The problem with this was that it crashed immediately with an error
> that my pulling distance was
> greater than 1/2 of the box vector.:
> 
> Fatal error:
> Distance of pull group 165 (5.353939 nm) is larger than 0.49 times the
> box size (5.395960)
> 
> Pretty obvious in retrospect. If I could get this error to go away,
> then everything should be fine because I have modified the code so that
> forces are zero at large displacements. However, I am worried that if I
> simply modify grompp to bypass this error then I might get some type of
> strange and possibly silent error in mdrun. Any thoughts on this are
> really appreciated.
> 
> For my second try, I used pull_geometry = direction-periodic (see more
> details below), but that also didn't work
> because if I set pull_vec1 = 0 0 1, then everything gets pulled to the
> upper part of the box (and LINCS errors
> ensue), rather than simply pulling away from the bilayer.
> 
> Pcoupl= berendsen
> pcoupltype   = semiisotropic
> compressibility= 4.5e-5 0
> pull = umbrella
> pull_geometry= direction-periodic
> pull_start   = no
> pull_ngroups = 9000
> pull_group0  = POPC
> 
> pull_group1  = r_1_&_OW
> pull_init1   = 1.9
> pull_k1  = 500
> pull_vec1= 0 0 1
> 
> pull_group2  = r_2_&_OW
> pull_init2   = 1.9
> pull_k2  = 500
> pull_vec2= 0 0 1
> 
> ... etc...
> 
> 
> If anybody has an idea about how I could get this to work with standard
> gromacs or with a modified version, I would be very grateful to hear
> your thoughts.
> 
> Thank you,
> Chris.
> 
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Re: [gmx-users] Proteins with ADP & ATP cofactors

[micheal j twin]

Dear Stephan,
thank you for your reply.

I'm performing some test with antechamber for a de-novo parametrization,
hope to see some good results with it.

> You probably have to do a hand job.  Look at the .itp/top files and then
the force field parmeters, here's not many atoms, so it would take only a
couple hours.
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[gmx-users] Re: About Potential energy calculation

[cyberjhon]

Hi Justin

Thanks for your answer. 
Actually, you are right and that is what I am doing now, but it is really
time consuming and it is like
double calculating because the potential energy  is computed during the MD. 

Any way thanks

John Michael



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Re: [gmx-users] About Potential energy calculation

[Justin Lemkul]

On 5/6/13 5:58 PM, jhon michael espinosa duran wrote:

Hi all

I am doing an NVE simulation of a protein immersed in water, and I want
to keep track of  the potential energy in the protein. Do you know how can I do 
it?.

I tried saving the energy of the protein ( the protein as an energy group) in 
the .edr file, but when I checked the file with g_energy, it does not give me 
the option of potential energy only for the protein, it  gives me the total 
potential energy.



The potential energy of a subset of atoms is not stored in the .edr file; only 
short-range nonbonded interactions can be decomposed by using energygrps.  There 
are a variety of reasons for doing so.  The easiest way to get the quantity you 
want is to use tpbconv create a .tpr file that contains only the protein and 
then re-calculate energies using mdrun -rerun on the existing trajectory.


-Justin

--


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Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] About Potential energy calculation

[jhon michael espinosa duran]

Hi all

I am doing an NVE simulation of a protein immersed in water, and I want 
to keep track of  the potential energy in the protein. Do you know how can I do 
it?.

I tried saving the energy of the protein ( the protein as an energy group) in 
the .edr file, but when I checked the file with g_energy, it does not give me 
the option of potential energy only for the protein, it  gives me the total 
potential energy.

I really appreciate your help. 

John M. Espinosa Duran
PhD student of Chemical Physics  
Indiana University

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Re: [gmx-users] REMD Statistics

[Mark Abraham]

On Mon, May 6, 2013 at 3:48 AM, Kong xq  wrote:

> Hi Mark,
>
>
> Thanks for your great help.  I am sorry for the negligence to state the
> variation value correctly( it should be 0.011 rather than 0.11). Does this
> somewhat small value indicate the generalized equilibrium achieved?


It might be consistent with it, but it is never diagnostic of it. FWIW, I
have never seen an REMD study that attempted to address whether generalized
equilibrium was achieved.

I will
> search the papers you suggested. I am wondering whether the histogram is
> the gold standard for effectively constructing REMD flow. Moreover, how to
> do the potential energy overlap analysis in Gromacs, from the edr file for
> each replica ？Does any tool avalible in Gromacs to do this job ?
>

g_energy to get the data for each replica, then your favorite analysis
package to form histograms, and graphing program to overlay the plots. The
histograms can be done with g_analyze.

Mark
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Re: [gmx-users] Still having issues analyzing normal-mode hessian

[Justin Lemkul]

On 5/6/13 2:16 PM, Bryan Roessler wrote:

Hello,

I have successfully generated a 945MB mtx hessian storing the normal modes
of a ~1500AA protein using mdrun with the "nm" integrator and no cutoffs.
However, when I try to analyze the normal modes and create trajectories
using g_nmeig, I can't seem to generate any output. I am running
g_nmeig_mpi_d  with the following options: "mpiexec_mpt g_nmeig_mpi_d -f
input.mtx -s NMA.tpr -of NMA_freq.xvg -ol NMA_val.xvg -v NMA_vec.trr" and


There is no point in trying to run in parallel; only mdrun is parallelized. 
That could be one source of problem.



have been letting it run a few times for up to 5 days on 128 Itanium nodes
with 120gb maximum memory. When the job finally aborts after running out of
cpu time, I get a standard output file that's about 8GB (which I am unable
to open). Is there a way to force g_nmeig to generate some output or at
least show me what is going on? Am I running it with the correct options?
There isn't a lot of documentation on these normal-mode specific programs
so I don't know how to begin troubleshooting.



Run interactively and try with a smaller data set, something that will consume 
very little memory, then scale up.


-Justin

--


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


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[gmx-users] Still having issues analyzing normal-mode hessian

[Bryan Roessler]

Hello,

I have successfully generated a 945MB mtx hessian storing the normal modes
of a ~1500AA protein using mdrun with the "nm" integrator and no cutoffs.
However, when I try to analyze the normal modes and create trajectories
using g_nmeig, I can't seem to generate any output. I am running
g_nmeig_mpi_d  with the following options: "mpiexec_mpt g_nmeig_mpi_d -f
input.mtx -s NMA.tpr -of NMA_freq.xvg -ol NMA_val.xvg -v NMA_vec.trr" and
have been letting it run a few times for up to 5 days on 128 Itanium nodes
with 120gb maximum memory. When the job finally aborts after running out of
cpu time, I get a standard output file that's about 8GB (which I am unable
to open). Is there a way to force g_nmeig to generate some output or at
least show me what is going on? Am I running it with the correct options?
There isn't a lot of documentation on these normal-mode specific programs
so I don't know how to begin troubleshooting.

Thanks,


*Bryan Roessler | Graduate Research Assistant*
UAB | The University of Alabama at Birmingham
*uab.edu/cmdb*
Knowledge that will change your world
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Re: [gmx-users] random seed in molecular dynamics

[Mark Abraham]

Google knows a lot more about that one than me ;-)

Mark


On Mon, May 6, 2013 at 9:16 AM, Preeti Choudhary <
preetichoudhary18111...@gmail.com> wrote:

> hey thanks Mark
> What do you mean by -the random seed is in a different variable.Can you
> please explain "the random seed"
>
>
>
> On Fri, May 3, 2013 at 1:32 PM, Mark Abraham  >wrote:
>
> > gen_vel controls the generation of random velocities. grompp follows it
> > (but I'd have to check the code to see what it does if you use grompp
> -t).
> > tprconv does not follow it.
> >
> > The random seed is in a different variable, but only does anything if
> > gen_vel=yes.
> >
> > I am not sure what the basis of your confusion about repeated calls to
> > grompp is.
> >
> > Mark
> >
> > On Fri, May 3, 2013 at 8:00 AM, Preeti Choudhary <
> > preetichoudhary18111...@gmail.com> wrote:
> >
> > > hey this is regarding random seed used in md.this is when it selects
> the
> > > intial velocity and selects from maxwell-istribution.but is it selects
> > only
> > > once or selects this random seed every time when grompp makes .tpr
> > > file.really confused about this random seed concept.can u clear my
> > > confusion??
> > >
> > > -thanks
> > > --
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[gmx-users] Can Gromacs do oscillatory shear?

[Yutian Yang]

Hi all, 

I am trying to preform oscillatory shear flow on Gromacs. Is there any existing 
commands/codes to do it or do I have to modify the code myself? If I have to 
modify code, where can I find the source code for deform? 

Thank you so much!

Shirley Young
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Re: [gmx-users] Tryptophan and tyrosine protonation

[Justin Lemkul]

Please use informative subject lines.  "No subject" often gets flagged as spam, 
and thus people who may be able to help you may never see your message.


On 5/6/13 7:58 AM, Sathish Kumar wrote:

I want to do simulation of protein at pH 12 so i have to deprotanate
tyrosine,tryphtophan.Can you please tell me how i can do with pdb2gmx
command



The answer is the same as with cysteine - either the force field will have 
parameters for such species or it won't.  If it doesn't, you have to implement 
suitable parameters; there is no magic that pdb2gmx can do for you.  Anionic 
tyrosine is more likely to have parameters available somewhere.  I have never 
heard of the tryptophan side chain being deprotonated under any conditions.


-Justin

--


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


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Re: [gmx-users] correct traj for water/ions density

[Justin Lemkul]

On 5/6/13 7:32 AM, gromacs query wrote:

Dear Justin,


You don't need to change the trajectory in any way to do density

measurements

I read sometime before in some paper: water density falls around polymer
(COM) at a distance nearly 4.5nm when it is in box of 10x10x10 nm. I assume
the polymer must be near the center of box so 5nm on either sides.

Then in my case (polymer at the box edge) how the box size will be
considered. I mean to say if my box is 10x10x10 and I calculate density it
will never fall around 5nm distance from polymer as my polymer is at edge
and will give different pattern.



Now the statement of your problem is more clear.  To calculate the density 
within the box, you do not need to do any manipulation.  For your purpose, where 
a fixed reference is convenient, there's certainly nothing wrong with centering 
the polymer.


-Justin

--


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


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[gmx-users] (no subject)

[Sathish Kumar]

I want to do simulation of protein at pH 12 so i have to deprotanate
tyrosine,tryphtophan.Can you please tell me how i can do with pdb2gmx
command
-- 
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M.SathishKumar
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Re: [gmx-users] Reax force field

[Sathish Kumar]

Thank you sir


On Mon, May 6, 2013 at 4:38 PM, Justin Lemkul  wrote:

>
>
> On 5/6/13 6:51 AM, Sathish Kumar wrote:
>
>> hai
>>   i would like to use Reax force field,can we use reax force field
>> in gromacs and if any one please tell to me weather reax ff is useful for
>> protein
>>
>>
> It won't be easy to use Reax, if it's even possible.  You would have to
> make some serious code modifications, both in terms of energy calculations
> and topology interpretation.  The former could possibly be achieved with
> tabulated potentials, but the latter would certainly have to be coded.
>  Reax doesn't use traditional bonds, and the Gromacs topology format
> doesn't know how to deal with bond orders in lieu of actual bonds.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
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Re: [gmx-users] Thiolate cysteine

[Sathish Kumar]

Thank you sir


On Mon, May 6, 2013 at 4:39 PM, Justin Lemkul  wrote:

>
>
> On 5/6/13 7:03 AM, Sathish Kumar wrote:
>
>>   I want to do simulation of protein at pH 12, in this case experimentally
>> reported that the disulphide bonds of protein was broken and sulphurs
>> become S negative  . Can you please tell me making of disulphide as S-
>>  and
>> S- is it correct and how to set force field to this.
>>
>
> Some force fields (like the Amber parameter sets and some others) have the
> CYM residue, which is the thiolate form of cysteine.  Find which force
> fields have this residue, read about their use, and make a choice based on
> what you find.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
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Re: [gmx-users] correct traj for water/ions density

[gromacs query]

Dear Justin,

>> You don't need to change the trajectory in any way to do density
measurements

I read sometime before in some paper: water density falls around polymer
(COM) at a distance nearly 4.5nm when it is in box of 10x10x10 nm. I assume
the polymer must be near the center of box so 5nm on either sides.

Then in my case (polymer at the box edge) how the box size will be
considered. I mean to say if my box is 10x10x10 and I calculate density it
will never fall around 5nm distance from polymer as my polymer is at edge
and will give different pattern.

regards,


On Mon, May 6, 2013 at 1:07 PM, Justin Lemkul  wrote:

>
>
> On 5/6/13 4:21 AM, gromacs query wrote:
>
>> Dear All,
>>
>> I want to calculate water and ions density around polymer. After MD I see
>> my polymer goes near the edges of box and rather some part is out of box.
>> So in order to calculate water and ion density I think polymer should be
>> near the center of box (please correct me if wrong)
>>
>>
> What you are seeing is a completely normal consequence of periodic
> boundary conditions.  You don't need to change the trajectory in any way to
> do density measurements; the resulting values will be the same before and
> after centering, since there is no "outside" or "center" of an infinite
> system.
>
> -Justin
>
>
>  So by doing this:
>>
>> trjconv -f NPT_mdrun.trr -s NPT_mdrun.tpr -o NPT_mdrun_trjconv.trr -pbc
>> mol
>> -center
>>
>> Select group for centering: I selected my polymer only
>> Select group for output: I selected all atoms (polymer + water + ions)
>>
>> Please let me know is this correct way of modifying trajectory to
>> calculate
>> water and ion density?
>>
>> regards,
>> Jiom
>>
>>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
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Re: [gmx-users] Thiolate cysteine

[Justin Lemkul]

On 5/6/13 7:03 AM, Sathish Kumar wrote:

  I want to do simulation of protein at pH 12, in this case experimentally
reported that the disulphide bonds of protein was broken and sulphurs
become S negative  . Can you please tell me making of disulphide as S-  and
S- is it correct and how to set force field to this.


Some force fields (like the Amber parameter sets and some others) have the CYM 
residue, which is the thiolate form of cysteine.  Find which force fields have 
this residue, read about their use, and make a choice based on what you find.


-Justin

--


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


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Re: [gmx-users] Reax force field

[Justin Lemkul]

On 5/6/13 6:51 AM, Sathish Kumar wrote:

hai
  i would like to use Reax force field,can we use reax force field
in gromacs and if any one please tell to me weather reax ff is useful for
protein



It won't be easy to use Reax, if it's even possible.  You would have to make 
some serious code modifications, both in terms of energy calculations and 
topology interpretation.  The former could possibly be achieved with tabulated 
potentials, but the latter would certainly have to be coded.  Reax doesn't use 
traditional bonds, and the Gromacs topology format doesn't know how to deal with 
bond orders in lieu of actual bonds.


-Justin

--


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


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Re: [gmx-users] (no subject)

[Erik Marklund]

I really don't think thats possible at the moment. All interactions in Reax, if 
I recall correctly, are dependent on bond order, which is not an implemented 
concept in gromacs.

Erik

On 6 May 2013, at 12:51, Sathish Kumar  wrote:

> hai
> i would like to use Reax force field,can we use reax force field
> in gromacs and if any one please tell to me weather reax ff is useful for
> protein
> 
> -- 
> regards
> M.SathishKumar
> -- 
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[gmx-users] (no subject)

[Sathish Kumar]

 I want to do simulation of protein at pH 12, in this case experimentally
reported that the disulphide bonds of protein was broken and sulphurs
become S negative  . Can you please tell me making of disulphide as S-  and
S- is it correct and how to set force field to this.
   Thank you.
-- 
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M.SathishKumar
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[gmx-users] (no subject)

[Sathish Kumar]

hai
 i would like to use Reax force field,can we use reax force field
in gromacs and if any one please tell to me weather reax ff is useful for
protein

-- 
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M.SathishKumar
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Re: [gmx-users] correct traj for water/ions density

[Justin Lemkul]

On 5/6/13 4:21 AM, gromacs query wrote:

Dear All,

I want to calculate water and ions density around polymer. After MD I see
my polymer goes near the edges of box and rather some part is out of box.
So in order to calculate water and ion density I think polymer should be
near the center of box (please correct me if wrong)



What you are seeing is a completely normal consequence of periodic boundary 
conditions.  You don't need to change the trajectory in any way to do density 
measurements; the resulting values will be the same before and after centering, 
since there is no "outside" or "center" of an infinite system.


-Justin


So by doing this:

trjconv -f NPT_mdrun.trr -s NPT_mdrun.tpr -o NPT_mdrun_trjconv.trr -pbc mol
-center

Select group for centering: I selected my polymer only
Select group for output: I selected all atoms (polymer + water + ions)

Please let me know is this correct way of modifying trajectory to calculate
water and ion density?

regards,
Jiom



--


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


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[gmx-users] Re: correct traj for water/ions density

[gromacs query]

Sorry forgot to add:::

by doing this I can see my polymer near the center of box


On Mon, May 6, 2013 at 11:21 AM, gromacs query wrote:

> Dear All,
>
> I want to calculate water and ions density around polymer. After MD I see
> my polymer goes near the edges of box and rather some part is out of box.
> So in order to calculate water and ion density I think polymer should be
> near the center of box (please correct me if wrong)
>
> So by doing this:
>
> trjconv -f NPT_mdrun.trr -s NPT_mdrun.tpr -o NPT_mdrun_trjconv.trr -pbc
> mol -center
>
> Select group for centering: I selected my polymer only
> Select group for output: I selected all atoms (polymer + water + ions)
>
> Please let me know is this correct way of modifying trajectory to
> calculate water and ion density?
>
> regards,
> Jiom
>
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[gmx-users] correct traj for water/ions density

[gromacs query]

Dear All,

I want to calculate water and ions density around polymer. After MD I see
my polymer goes near the edges of box and rather some part is out of box.
So in order to calculate water and ion density I think polymer should be
near the center of box (please correct me if wrong)

So by doing this:

trjconv -f NPT_mdrun.trr -s NPT_mdrun.tpr -o NPT_mdrun_trjconv.trr -pbc mol
-center

Select group for centering: I selected my polymer only
Select group for output: I selected all atoms (polymer + water + ions)

Please let me know is this correct way of modifying trajectory to calculate
water and ion density?

regards,
Jiom
-- 
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Re: [gmx-users] constant protonation state MD

[Jesper Sørensen]

Then there is a wealth of papers that describe secondary structure 
determination from the experimental point of view that you should look for.
NMR and CD would be the first obvious methods that come to mind, but there are 
probably others as well.
These should be able to help you validate or invalidate your modeling 
observations. 

Best of luck!
Jesper

On May 5, 2013, at 9:47 PM, shahid nayeem  wrote:

> It is a peptide.
> Shahid
> 
> 
> On Mon, May 6, 2013 at 4:46 AM, Jesper Sørensen  wrote:
> 
>> Shahid,
>> 
>> This must be system dependent then because there are experimental methods,
>> e.g. NMR and CD, that can help determine the secondary structure of
>> proteins/peptides are various pH ranges.
>> What is your system? A peptide? A globular protein?
>> 
>> Best,
>> Jesper
>> 
>> On May 3, 2013, at 7:33 PM, shahid nayeem  wrote:
>> 
>>> Thanks a lot Erik and Baptista
>>> I am interested in simulating the change in secondary structure which is
>>> supposed to be influenced by the change in the pH environment of the
>> cell.
>>> Experimentally it is not known but it has been proposed by many that the
>>> change in pH leads to change in conformation. I did constant protonation
>>> state MD at two different pH. I got an alpha helix converting to beta
>> sheet
>>> at higher pH but not at lower pH. I am bothered to prove the reliability
>> of
>>> the simulation results as experimentally it cant be established.
>>> 
>>> Shahid
>>> 
>>> 
>>> On Sat, May 4, 2013 at 5:46 AM,  wrote:
>>> 
 Hi Shahid,
 
 As Erik said, it depends... on your system, on the process you are
 studying in that system, on the property you think it's relevant to
>> study
 that process, etc.
 
 If your question refers to the (de)protonation of acidic and basic
>> groups
 usually occuring in aqueous solution, there are methods to perform what
>> is
 called constant-pH MD, where the protonation states of those groups
>> change
 in a discrete or continuous way along the simulation. If you are
 interested, start with the corresponding GROMACS how-to (
 http://www.gromacs.org/**Documentation/How-tos/**Constant_pH_Simulation
>> )
 and then search the literature.
 
 In any case, you don't need any of that fancy stuff unless you have
 reasons to think that the properties you want to study in your system
>> are
 strongly dependent on protonation-conformation coupling effects. In some
 cases you may be suspicious about the effect of the protonation state of
 one group (e.g., a histidine), but that can be simply tested by
>> performing
 two constant-protonation MD simulations, one for each state (you can
>> even
 try to use a linear response approximation on top of that). But in most
 cases you don't need even that.
 
 For what it's worth: I was one of the first to develop and apply
 constant-pH MD and I don't bother to use it most of the time... :)
 
 Best,
 Antonio
 
 
 On Fri, 3 May 2013, Erik Marklund wrote:
 
 Yes that's what lambda dynamics does. I mentioned it since it addresses
> the interplay between protonation and structure. So to answer your
>> original
> question: it depends.
> 
> Erik
> 
> On 3 May 2013, at 15:27, shahid nayeem  wrote:
> 
> If I know correctly in lambda dynamics the dynamics of
>> protonation/deprotonation equilibria is accounted for while my
>> question
>> relates to the typical constant protonation MD where each titratable
>> group
>> remains in one protonation state throughout the simulation. Please
>> educate
>> me
>> Shahid
>> 
>> 
>> On Fri, May 3, 2013 at 6:22 PM, Erik Marklund 
>> wrote:
>> 
>> I don't have one in mind. It's a delicate question and perhaps I
>>> shouldn't
>>> have phrased it the way I did. Nevertheless, the pKa of most side
>> chains
>>> mean that their protonation will be dominated by one state for most
>> pH
>>> values. pKa-shifts and complicated interplay between protonation and
>>> structure cause exceptions to this and you should be aware that such
>>> things
>>> may in some cases be important. Also consider the timescales of
>>> pH-depedent
>>> structural changes and the length of your simulations. You could
>> check
>>> out
>>> the papers on lambda dynamics by C. Brooks III for an interesting
>> take
>>> on
>>> sampling multiple protonation states.
>>> 
>>> Best,
>>> 
>>> Erik
>>> 
>>> On 3 May 2013, at 14:05, shahid nayeem  wrote:
>>> 
>>> Thanks a lot Erik. Could I get some reference based on which you say
 that
 much of the structural biology will be largely unaffected.
 
 Shahid
 
 
 On Fri, May 3, 2013 at 1:05 PM, Erik Marklund >> 
 
>>> wrote:
>>> 

[gmx-users] Equilibrated system explodes after ~200ns?

[Trayder]

Hi all,
My simulation is composed of 2 protein chains wrapped around a lipid disk
composed of a dozen different lipid types, water and ions in a 15nm cube.
The protein encircles the mixed composition lipid disk.
I've got 4 duplicate simulations with velocities generated from a different
random seed.
The starting structure for these simulations was taken from the end of a
previous 200ns simulation (same settings but bigger box) which ended
normally.
I am using gromacs 4.6, with the gromos54a7 force field. No gpus.

The first simulation exploded (a few atoms fly off into the distance leaving
the rest intact) shortly before 150ns, two more have crashed shortly before
200ns. 1 is still running. Restarting a simulation has it crash at a
different point.

Over 3 steps of escalating LINCS warnings I get a warning followed by a
fatal error





The atoms initially involved in the LINCS warnings correspond to atoms
around a double bond in a single lipid tail. Specifically in linoleic and
linolenic (2 or 3 double bonds in sequence). The parameters used were
adapted from the packaged POPC parameters using the same bond types from
ffbonded.itp

Energy graphs seem to indicate that the system is equilibrated.
Does anyone have any ideas what's going on here?
Thanks in advance,
-Trayder

P.S. mdp file












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Re: [gmx-users] random seed in molecular dynamics

[Preeti Choudhary]

hey thanks Mark
What do you mean by -the random seed is in a different variable.Can you
please explain "the random seed"



On Fri, May 3, 2013 at 1:32 PM, Mark Abraham wrote:

> gen_vel controls the generation of random velocities. grompp follows it
> (but I'd have to check the code to see what it does if you use grompp -t).
> tprconv does not follow it.
>
> The random seed is in a different variable, but only does anything if
> gen_vel=yes.
>
> I am not sure what the basis of your confusion about repeated calls to
> grompp is.
>
> Mark
>
> On Fri, May 3, 2013 at 8:00 AM, Preeti Choudhary <
> preetichoudhary18111...@gmail.com> wrote:
>
> > hey this is regarding random seed used in md.this is when it selects the
> > intial velocity and selects from maxwell-istribution.but is it selects
> only
> > once or selects this random seed every time when grompp makes .tpr
> > file.really confused about this random seed concept.can u clear my
> > confusion??
> >
> > -thanks
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