[gmx-users] Molecule specific explosion

[Eric Smoll]

Hello Gromacs Users,

I have constructed a multi-component solution and, during energy
minimization, one molecule type is radically deforming under ~ 0.2 ps. All
molecules of this type "explode" simultaneously. Looking over the topology,
all the atoms in this molecules appear to have correct forcefield
assignments. I am writing to ask if anyone might have a suggestion on how I
can identify the origin of this problem.

Best,
Eric
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Re: [gmx-users] pdb2gmx and periodic molecule

[Alex]

Well, none of us in this project have the scripting skills necessary for this, that's sort of the problem...

Thanks,

Alex





>


Hi Alex,
I think the best way is to extend the chain, such that you get an overlap between both ends. So for a stretch of DNA
ACGT
You would generate 
TACGTA
Then you strip off the terminal atoms and rewire the links over the boundary. It requires renumbering the topology and at first looks a bit cumbersome, but this ensures all the links are correct and the modifications of the termini have no effect, and it's not very hard to script. And, of course, scripting it is a one time effort to avoid doing it manually later.
Cheers,
Tsjerk
On Apr 26, 2015 5:55 AM, "Alex"  wrote:

JL> The force field parameters for a phosphodiester are the same in a linear, finite
JL> DNA as they will be in your infinite chain.

I didn't mean that anything would need to be changed in the description of residues. The FF handles a
finite chain perfectly.

JL> The problem is in telling pdb2gmx
JL> "don't link i,i+1 here, instead link i,i+(some number of intervening nucleotides)."

This is exactly what I meant, the linking. Is there a way to achieve this
without messing with the code? I just haven't looked at the code, so
if you think I'm being a cheeky little bastard, I'll accept that. :)

Thanks,

Alex


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-- 
Best regards,
 Alex                            mailto:nedoma...@gmail.com



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[gmx-users] on the MDP options

[Brett]

Dear All,
 
In the on-line lysozyme tutorial, it gives a series of mdp files. But it 
meantioned for different force fields the options should be different.
 
Will you please tell me regardless of force fields, whether all the 
cutoff-scheme can be Verlet? Besides I can change the rcoulomb and rvdw fom 1.0 
to 1.4, what else should I change on the basis of the on-line tutorial MDP 
files, with the difference of the force fields?
 
I am looking forward to getting your reply.
 
Brett
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Re: [gmx-users] how to name HIS in the input pdb for the pdb2gmx

[Mark Abraham]

Hi,

Files in fixed-column formats use the column widths to separate elements.
They don't use white space at the same time, for the same job! Try it and
see ;-)

Mark
On 26/04/2015 6:29 am, "Brett"  wrote:

> Dear All，
>
> If we change HIS188 in Chain B to HISE188 in Chain B, before change the
> PDB looks like
> "HIS B  188", but after change the PDB will look like "HISEB 188", which
> makes thereis no space between "HISE" and "Bchain". I do not know whether
> pdb2gmx can recognize HISEB 188, or we process it in some other way.
>
> I am looking forward to getting a reply from you.
>
> Brett
>
>
>
>
>
>
>
>
> At 2015-04-26 11:08:19, "Justin Lemkul"  wrote:
> >
> >
> >On 4/25/15 11:05 PM, Brett wrote:
> >> Dear All,
> >>
> >> For gromacs, for HIS residues there are HISD,HISE and HISH. In the
> original PDB file, are HIS residues are written as HIS. If based on
> necessity, I change exactly some HIS to HISD, some HIS to HISE and some HIS
> to HISH,the coordinate lines contaning HISD,HISE and HISH will not aling
> with all the other coordinate lines. Does pdb2gmx recognize these
> non-aligned coordinate lines? Or what other strategy you recommend me to
> take so that pdb2gmx can recognize HISD,HISE and HISH?
> >>
> >
> >Do the replacement properly and don't screw up column alignment.  It
> needs to be
> >correct for proper interpretation of the coordinates.
> >
> >-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] Molecule specific explosion

[Mark Abraham]

Hi,

Look at the whole molecule topology. Don't ignore any warnings.

Mark
On 26/04/2015 9:38 am, "Eric Smoll"  wrote:

> Hello Gromacs Users,
>
> I have constructed a multi-component solution and, during energy
> minimization, one molecule type is radically deforming under ~ 0.2 ps. All
> molecules of this type "explode" simultaneously. Looking over the topology,
> all the atoms in this molecules appear to have correct forcefield
> assignments. I am writing to ask if anyone might have a suggestion on how I
> can identify the origin of this problem.
>
> Best,
> Eric
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[gmx-users] a question related to gmx energy minimization

[Brett]

Dear All,
 
I just run the command gmx energy -f em.edr -o potential.xvg for my energy 
minimization step MD, but I find the RMSD given by this command is 142611, 
which I regard to be too high.
 
Will you please explain to me what leads to the so high RMSD (Err.Est is 53000, 
Tot-Drift is -341107 KJ/mol)?
 
I am looking forward to getting your reply.
 
Brett
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[gmx-users] free energy

[fatemeh ramezani]

Dear gmx-usersI want to calculate free energy of binding of ligand to Au 
surface in 8 ns simulation. I considered 7 lambda (lambda= 0, 0.2, 0.4, 0.6, 
0.8, 0.9, 1) and for every lambda a mdp file. for example lambda-0 mdp file:
title   =  n.pdb restraining
cpp =  /lib/cpp
constraints =  all-bonds
constraint_algorithm = lincs
lincs_order = 4
lincs_iter  = 1
integrator  =  sd 
dt  =  0.0008
nsteps  =  250
nstcomm =  100
nstcalcenergy   =  100
nstdhdl =  100
comm_mode   =  
nstxout =  5000
nstvout =  5000
nstfout =  0
nstlog  =  5000
nstenergy   =  5000
nstlist =  10
ns_type =  grid
rlist   =  1.4
;rlistlong   =  2
coulombtype =  PME
rcoulomb    =  1.4
rcoulomb-switch =  0.8
rvdw    =  1
vdwtype =  shift
rvdw-switch =  0.9
fourierspacing  =  0.12
fourier_nx  =  0
fourier_ny  =  0
fourier_nz  =  0
pme_order   =  6
ewald_rtol  =  1e-5
optimize_fft    =  yes
  
; Berendsen temperature coupling is on in three groups
Tcoupl  =  V-rescale
tau_t   =  0.1   0.1
tc-grps            =  Protein   Non-Protein
ref_t   =  300   300
; Pressure coupling is  on
;Pcoupl  =  berendsen
Pcoupl  =  Parrinello-Rahman
Pcoupltype =  isotropic
tau_p   =  5
compressibility =  4.5e-5
ref_p   =  1.0
; Generate velocites is on at 300 K.
gen_vel =  yes
gen_temp    =  300.0
gen_seed    =  173529
energygrps  = Protein  Sol 
freezegrps  = AU  AUI   AUC
freezedim   = Y Y Y  Y Y Y  Y Y Y
free-energy = yes
couple-moltype  = Protein2
init-lambda = 0
sc-power    = 1
sc-sigma    = 0.3
sc-alpha    = 1
couple-intramol =  no
couple-lambda1  = vdwq
couple-lambda0  = none
foreign-lambda  = &ALL_LAMBDAS$
As you can see dt= 0.0008, for 8 ns simulation, I should take the nstep of each 
Lambda 1 ( or I should divide 8 ns  between 7  Lambda)? In other words, the 
simulation time for each of the 7 lambda should be 8 ns or every lambda 
simulation time should be considered so that the total simulation time of 
lambdas be 8 ns?
I hope I could correctly ask my question. I would greatly appreciate your 
response to my question.
 Fatemeh Ramezani
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Re: [gmx-users] a question related to gmx energy minimization

[Tsjerk Wassenaar]

Hi Brett,

Too high for what?

You do EM because you just built (part of) your system, and in doing so
introduced clashes and non-ideal geometries. These lead to high potential
energy, so you relax them with EM. What you see is how much the system
relaxed. Noone usually cares how much potential energy was lost during EM.
The thing that matters is whether the resulting system is relaxed enough to
run the simulation.

Cheers,

Tsjerk

On Sun, Apr 26, 2015 at 2:43 PM, Brett  wrote:

> Dear All,
>
> I just run the command gmx energy -f em.edr -o potential.xvg for my energy
> minimization step MD, but I find the RMSD given by this command is 142611,
> which I regard to be too high.
>
> Will you please explain to me what leads to the so high RMSD (Err.Est is
> 53000, Tot-Drift is -341107 KJ/mol)?
>
> I am looking forward to getting your reply.
>
> Brett
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>



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Re: [gmx-users] a question related to gmx energy minimization

[Brett]

Dear Tsjerk,
 
Will you please explain to me why the RMSD in this step is so large? For this 
reason I think there is something wrong.
 
I am looking forward to getting a reply from you.
 
Brett








At 2015-04-26 20:59:59, "Tsjerk Wassenaar"  wrote:
>Hi Brett,
>
>Too high for what?
>
>You do EM because you just built (part of) your system, and in doing so
>introduced clashes and non-ideal geometries. These lead to high potential
>energy, so you relax them with EM. What you see is how much the system
>relaxed. Noone usually cares how much potential energy was lost during EM.
>The thing that matters is whether the resulting system is relaxed enough to
>run the simulation.
>
>Cheers,
>
>Tsjerk
>
>On Sun, Apr 26, 2015 at 2:43 PM, Brett  wrote:
>
>> Dear All,
>>
>> I just run the command gmx energy -f em.edr -o potential.xvg for my energy
>> minimization step MD, but I find the RMSD given by this command is 142611,
>> which I regard to be too high.
>>
>> Will you please explain to me what leads to the so high RMSD (Err.Est is
>> 53000, Tot-Drift is -341107 KJ/mol)?
>>
>> I am looking forward to getting your reply.
>>
>> Brett
>> --
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>> posting!
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>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
>
>-- 
>Tsjerk A. Wassenaar, Ph.D.
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[gmx-users] on the xmgrac for gromacs

[Brett]

Dear All,
 
For the grpmacs analysis purpose, from the official GRACE site I have 
downloaded and installed different versions of GRACE, some was said to 
definitely contains xmgrace. But after installation, none contains xmgrace, 
they contain grace or gr in the bin folder. After I invoke the grace or gr, 
both needs me input commands, and if I input grace -nxy potential.xvg, they did 
not work.
 
My workstation is a red hat linux system, and I do not know whether there is X  
windows installed.
 
Will you please let me know how to have my " xmgrace -nxy potential.xvg" 
function works?
 
Brett

 
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Re: [gmx-users] on the xmgrac for gromacs

[abhijit Kayal]

the command is xmgrace, try with xmgrace -nxy.

On Sun, Apr 26, 2015 at 7:01 AM, Brett  wrote:

> Dear All,
>
> For the grpmacs analysis purpose, from the official GRACE site I have
> downloaded and installed different versions of GRACE, some was said to
> definitely contains xmgrace. But after installation, none contains xmgrace,
> they contain grace or gr in the bin folder. After I invoke the grace or gr,
> both needs me input commands, and if I input grace -nxy potential.xvg, they
> did not work.
>
> My workstation is a red hat linux system, and I do not know whether there
> is X  windows installed.
>
> Will you please let me know how to have my " xmgrace -nxy potential.xvg"
> function works?
>
> Brett
>
>
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-- 
Abhijit kayal
Research Scholar
Theoretical Chemistry
IIT Kanpur
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Re: [gmx-users] on the xmgrac for gromacs

[Brett]

The issue is, no mater grace or xmggrace I download, I cannot have the xmgrace 
exe file in the corresponding bin folder produced.
 
Thus will you tell me which version of grace  has the xmgrace after unpack and 
installation?
 
Brett



At 2015-04-26 23:09:23, "abhijit Kayal"  wrote:
>the command is xmgrace, try with xmgrace -nxy.
>
>On Sun, Apr 26, 2015 at 7:01 AM, Brett  wrote:
>
>> Dear All,
>>
>> For the grpmacs analysis purpose, from the official GRACE site I have
>> downloaded and installed different versions of GRACE, some was said to
>> definitely contains xmgrace. But after installation, none contains xmgrace,
>> they contain grace or gr in the bin folder. After I invoke the grace or gr,
>> both needs me input commands, and if I input grace -nxy potential.xvg, they
>> did not work.
>>
>> My workstation is a red hat linux system, and I do not know whether there
>> is X  windows installed.
>>
>> Will you please let me know how to have my " xmgrace -nxy potential.xvg"
>> function works?
>>
>> Brett
>>
>>
>> --
>> Gromacs Users mailing list
>>
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>> posting!
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>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
>
>-- 
>Abhijit kayal
>Research Scholar
>Theoretical Chemistry
>IIT Kanpur
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Re: [gmx-users] a question related to gmx energy minimization

[Justin Lemkul]

On 4/26/15 9:53 AM, Brett wrote:

Dear Tsjerk,

Will you please explain to me why the RMSD in this step is so large? For this 
reason I think there is something wrong.



No, there's nothing wrong; the analysis in this case is meaningless.

Energy minimization inherently makes large (orders of magnitude in many cases) 
changes to the potential as the structure is relaxed.  An average energy over 
the course of this process has absolutely no physical meaning.


-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] free energy

[Justin Lemkul]

On 4/26/15 8:54 AM, fatemeh ramezani wrote:

Dear gmx-usersI want to calculate free energy of binding of ligand to Au 
surface in 8 ns simulation. I considered 7 lambda (lambda= 0, 0.2, 0.4, 0.6, 
0.8, 0.9, 1) and for every lambda a mdp file. for example lambda-0 mdp file:
title   =  n.pdb restraining
cpp =  /lib/cpp
constraints =  all-bonds
constraint_algorithm = lincs
lincs_order = 4
lincs_iter  = 1
integrator  =  sd
dt  =  0.0008
nsteps  =  250
nstcomm =  100
nstcalcenergy   =  100
nstdhdl =  100
comm_mode   =
nstxout =  5000
nstvout =  5000
nstfout =  0
nstlog  =  5000
nstenergy   =  5000
nstlist =  10
ns_type =  grid
rlist   =  1.4
;rlistlong   =  2
coulombtype =  PME
rcoulomb=  1.4
rcoulomb-switch =  0.8
rvdw=  1
vdwtype =  shift
rvdw-switch =  0.9
fourierspacing  =  0.12
fourier_nx  =  0
fourier_ny  =  0
fourier_nz  =  0
pme_order   =  6
ewald_rtol  =  1e-5
optimize_fft=  yes

; Berendsen temperature coupling is on in three groups
Tcoupl  =  V-rescale
tau_t   =  0.1   0.1
tc-grps=  Protein   Non-Protein
ref_t   =  300   300
; Pressure coupling is  on
;Pcoupl  =  berendsen
Pcoupl  =  Parrinello-Rahman
Pcoupltype =  isotropic
tau_p   =  5
compressibility =  4.5e-5
ref_p   =  1.0
; Generate velocites is on at 300 K.
gen_vel =  yes
gen_temp=  300.0
gen_seed=  173529
energygrps  = Protein  Sol
freezegrps  = AU  AUI   AUC
freezedim   = Y Y Y  Y Y Y  Y Y Y
free-energy = yes
couple-moltype  = Protein2
init-lambda = 0
sc-power= 1
sc-sigma= 0.3
sc-alpha= 1
couple-intramol =  no
couple-lambda1  = vdwq
couple-lambda0  = none
foreign-lambda  = &ALL_LAMBDAS$
As you can see dt= 0.0008, for 8 ns simulation, I should take the nstep of each 
Lambda 1 ( or I should divide 8 ns  between 7  Lambda)? In other words, the 
simulation time for each of the 7 lambda should be 8 ns or every lambda 
simulation time should be considered so that the total simulation time of 
lambdas be 8 ns?


How have you predetermined that you want 8 ns total, split over 7 states?  You 
should do some test runs to assess convergence and determine how much sampling 
per state is necessary, rather than just assume a certain time.


-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] Using thermostats to create temperature gradient in system

[Suzen, Mehmet]

Hi Agnivo,

Temperature gradient means non-equilibrium MD (NEMD)

See notes from Prof. Martini:
https://nanohub.org/resources/7582/download/Martini_L10_NonequilibruimMD.pdf

What observable would you like to measure? Lets say you want to
measure observable A.

One "procedure" I can think of:

1.  You can run all system at T=300K with NVT. After equilibrium,
continue running all system at T=400K with freezing solvent group.
See, to how to freeze a group,
http://manual.gromacs.org/online/mdp_opt.html#neq

To get a good statistic, you need to repeat this procedure K times as
"solvent thermal wall" configuration  would be
different at each simulation.

100ps? Where did you get that? You need to see how observable A
behaves to see if 100ps is enough,  time average. And see how 
behaves in K different cases.


2. Similar to previous procedure but this time after freezing solvent
group, run system in NVE. Again, you need to repeat this
many times to get a good statistic. Similarly monitor observable A to
see if 500ps is enough.

However,  I suggest you to talk to someone having NEMD experience as
this procedure is just a heuristic approach.

-m
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Re: [gmx-users] Constraints and Energy Minimization

[Eric Smoll]

Hello Dr Lemkul,

Thank you for the clarification. To summarize: If I have a bond between two
atoms and one of the atoms has a topology "atom" field that begins with the
letter "H," "constraints=h-bonds" will transform it into a constraint.

I have another question. When specifying this "constrained bond," I have an
equilibrium distance but I do not have a force-constant. Is it irrelevant
what value I choose for the force constant if I apply constraints to that
bond?

Best,
Eric

On Sat, Apr 25, 2015 at 9:07 PM, Justin Lemkul  wrote:

>
>
> On 4/25/15 11:01 PM, Eric Smoll wrote:
>
>> Hello Dr Lemkul,
>>
>> Thank you for the rapid response. It is much appreciated.
>>
>> On the subject of specifying constraints, how does the mdp keyword-value
>> pair: "constraints=h-bonds" work?  How are the bonds with hydrogen
>> detected?
>>
>>
> By atom name.  If the first character is 'H' it is converted to a
> constraint.
>
>  Here are a few lines from ffnonbonded.itp in the oplsaa.ff. The atoms
>> shown
>> are for custom hydrogen additions to the opls forcefield. Note that the
>> "bond_type" field begins with the element letter (in this case, "C" and
>> "H") and has a suffix.
>>
>> [ atomtypes ]
>>
>> ; full atom descriptions are available in ffoplsaa.atp
>> ; name  bond_typemasscharge   ptype  sigma  epsilon
>>opls_972CA_C   6  12.01100-0.130   A3.55000e-01
>>   2.92880e-01  ;SIG
>>opls_973HA_C   1   1.00800 0.210   A2.42000e-01
>>   1.25520e-01  ;SIG
>>
>>
> This is only relevant for specifying, e.g. a bond in [bondtypes] between
> CA_C and HA_C.  If I understand your original question right, there are no
> parameters for these bonds, so this really isn't relevant.
>
>
>> Similarly, here are a few lines from the topology I have built. Note that
>> I
>> prefer to have the "atom" field list the chemical element (again "C" and
>> "H") followed by a numerical suffix. In general my ffnonbonded "bond_type"
>> field and the topology "atom" field do not match and are never just
>> labeled
>> with the element name.
>>
>> [ atoms ]
>> ;   nr   type  resnr residue  atom   cgnr charge   mass  typeB
>> chargeB  massB
>>1096   opls_972 42CCC C5332  -0.13 12.011   ;
>> qtot -13.07
>>1097   opls_973 42CCC H6332   0.21  1.008   ;
>> qtot -12.86
>>
>> Will "constraints=h-bonds" correctly identify C-H bonds in my system
>> without manually adding to the topology?
>>
>>
> Yes.  If a bond is listed between the atoms, it will be converted.
>
>
> -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] Constraints and Energy Minimization

[Justin Lemkul]

On 4/26/15 3:40 PM, Eric Smoll wrote:

Hello Dr Lemkul,

Thank you for the clarification. To summarize: If I have a bond between two
atoms and one of the atoms has a topology "atom" field that begins with the
letter "H," "constraints=h-bonds" will transform it into a constraint.



Exactly.


I have another question. When specifying this "constrained bond," I have an
equilibrium distance but I do not have a force-constant. Is it irrelevant
what value I choose for the force constant if I apply constraints to that
bond?



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] Using thermostats to create temperature gradient in system

[Agnivo Gosai]

Hello users,

Thanks a lot Suzen for an insightful suggestion. My protein and solvent
have been equilibrated at 300 K in an NVT ensemble.

I raised the temperature of protein gradually by using simulated annealing
to 400 K and the solvent has been kept at 300 K.

Now I wish to get a temperature gradient such that the temperature of the
protein comes down by exchanging heat with the solvent to 300 K.

So as per your suggestion , do I need to freeze the solvent group so that
its position will not be updated and hence it will have the same
temperature ??

For the protein if I do not use a thermostat , GROMACS will give error
message. So how do I fix this problem ?

Or, should I freeze the protein instead and use a thermostat on the solvent
?

I am trying both of these as I write this mail.


Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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Re: [gmx-users] Using thermostats to create temperature gradient in system

[Suzen, Mehmet]

Hi Agnivo;

Yes, the idea of freezing the solvent or the protein in many times is
to sample the "non-equilibrium thermal process". It will remain in the
target temperature on average, over many fixed configurations obtained
by different NVT runs (equilibrium runs). But you may need to run this
many K times to get a good statistic as I said. Concerning NVE, yes,
do the same fixing approach with the protein. But as I mentioned
earlier, this is quite heuristic approach, I suggest you to talk with
any faculty member having background in non-equilibrium processes if
this approach mimics what you need.

Best,
-m
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Re: [gmx-users] Using thermostats to create temperature gradient in system

[Agnivo Gosai]

Hello Users,

This is in relation to my previous posts.

I am looking to replicate the figure below :

​
 tempgradient.png

​
Basically I am following this paper for my work :

​
 Lervik_ProtWatInterHT_2009.pdf

​
Look at figure 6 of the paper.

My system has water at 300 K and protein at 400 K. The authors of the paper
describe that they removed the thermostat from the protein and let it relax
keeping the solvent (water) at 300 K.

But if I remove thermostat , I get GROMACS error and using freeze groups I
am not getting any temperatures as the molecules are not moving.

I can not understand how to model this system. Any suggestions will be
helpful. I am doing a literature search but till now it is not fruitful.

Best,
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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Re: [gmx-users] a question related to gmx energy minimization

[Brett]

Dear Justin,
 
I mean why the RMSD is such huge. Does it mean in the energy mminimization step 
the protein has moved from point A to point B which is long long distance away 
from point A but, although the protein has been continously embedded in water? 
If the RMSD is above several thousands, it would mean the protein conformation 
after energy minimization would be absolutely different from the input pdb for 
the pdb2gmx.
 
I am looking forward to getting a clarification.
 
Brett

 




At 2015-04-27 00:00:22, "Justin Lemkul"  wrote:
>
>
>On 4/26/15 9:53 AM, Brett wrote:
>> Dear Tsjerk,
>>
>> Will you please explain to me why the RMSD in this step is so large? For 
>> this reason I think there is something wrong.
>>
>
>No, there's nothing wrong; the analysis in this case is meaningless.
>
>Energy minimization inherently makes large (orders of magnitude in many cases) 
>changes to the potential as the structure is relaxed.  An average energy over 
>the course of this process has absolutely no physical meaning.
>
>-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] a question related to gmx energy minimization

[Justin Lemkul]

On 4/26/15 7:42 PM, Brett wrote:

Dear Justin,

I mean why the RMSD is such huge. Does it mean in the energy mminimization step 
the protein has moved from point A to point B which is long long distance away 
from point A but, although the protein has been continously embedded in water? 
If the RMSD is above several thousands, it would mean the protein conformation 
after energy minimization would be absolutely different from the input pdb for 
the pdb2gmx.

I am looking forward to getting a clarification.



Don't confuse the RMSD of the coordinates with the RMSD of the potential energy 
data series.


What gmx energy is printing is what you asked for - an analysis of the potential 
energy, so RMSD here is the RMSD of the energy values.  Even small changes in 
the structure can have very large effects on the energy.  You may go from +10^6 
before EM to -10^6 after EM.  That's 12 orders of magnitude difference in the 
energy, but your protein's RMSD is probably a fraction of an Angstrom.


-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] Using thermostats to create temperature gradient in system

[Justin Lemkul]

On 4/26/15 7:07 PM, Agnivo Gosai wrote:

Hello Users,

This is in relation to my previous posts.

I am looking to replicate the figure below :

​
  tempgradient.png

​
Basically I am following this paper for my work :

​
  Lervik_ProtWatInterHT_2009.pdf

​
Look at figure 6 of the paper.

My system has water at 300 K and protein at 400 K. The authors of the paper
describe that they removed the thermostat from the protein and let it relax
keeping the solvent (water) at 300 K.

But if I remove thermostat , I get GROMACS error and using freeze groups I
am not getting any temperatures as the molecules are not moving.



You'll have to show us what you're doing to "get GROMACS error" (what error? 
what were your input settings? Don't make us guess!)


Freezing groups means they have no temperature and they don't move.  This 
certainly isn't what you want.



I can not understand how to model this system. Any suggestions will be
helpful. I am doing a literature search but till now it is not fruitful.



Setting tau_t = -1 for the protein tc-grp will "remove" the thermostat; e.g. not 
couple it.  This sounds like what you want.


-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] Using thermostats to create temperature gradient in system

[Agnivo Gosai]

Hello all,

Thanks to Dr. Lemkul for asking.

This is what I did to reach my present state :

(a) Prepared the topology of the system using GROMOS96 43a2 ff and energy
minimized the system after solvation using steepest descent algorithm.

(b) Did a position restrained ( protein ) 5 ns


Fatal error:
2936 atoms are not part of any of the T-Coupling groups
For more information and tips for troubleshooting, please check the GROMACS

Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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Re: [gmx-users] Using thermostats to create temperature gradient in system

[Justin Lemkul]

On 4/26/15 8:14 PM, Agnivo Gosai wrote:

Hello all,

Thanks to Dr. Lemkul for asking.

This is what I did to reach my present state :

(a) Prepared the topology of the system using GROMOS96 43a2 ff and energy
minimized the system after solvation using steepest descent algorithm.

(b) Did a position restrained ( protein ) 5 ns


Fatal error:
2936 atoms are not part of any of the T-Coupling groups
For more information and tips for troubleshooting, please check the GROMACS



This means your tc-grps are set up incorrectly, but again you haven't provided 
your actual settings (copy and paste your .mdp when reporting problems - always).


-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] Using thermostats to create temperature gradient in system

[Agnivo Gosai]

Hello all,

Thanks to Dr. Lemkul for asking.

This is what I did to reach my present state :

(a) Prepared the topology of the system using GROMOS96 43a2 ff and energy
minimized the system after solvation using steepest descent algorithm.

(b) Did a position restrained ( protein restrained ) 5 ns NVT equilibration
using V-rescale thermostat at target temp. of 300 K.

(c) Then I kept the solvent at 300 K in a NVT ensemble and heated the
protein only by simulated annealing over 500 ps , to 400K. I checked the
individual temperatures and found that it was achieved.

(d) Then as mentioned in the paper if I remove the thermostat on the
protein then "grompp" gives the following error :-

Fatal error:
2936 atoms are not part of any of the T-Coupling groups
For more information and tips for troubleshooting, please check the GROMACS

I want to let my protein loose heat and thus go down a temp. gradient while
the solvent i.e. water stays at 300 K. However , I am unable to do this. If
I do not specify any thermostat in a NVT ensemble it becomes NVE and I only
get a single temperature profile.

Any hints as to how I can achieve my objective ?

Sorry for the previous incomplete post.


Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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Re: [gmx-users] Using thermostats to create temperature gradient in system

[Agnivo Gosai]

Hello,

I am copy pasting my "mdp" file for the last step of my procedure :

Here I am not using any freeze group.

; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 5; 100 ps
dt  = 0.002 ; 2 fs
energygrps  = Protein Non-Protein
; Output control
nstxout = 10
nstvout = 10
nstlog  = 10
nstenergy   = 10
nstxtcout   = 50
; Bond parameters
continuation= yes   ; after trial 400 K
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   = 1.4   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.4   ; short-range electrostatic cutoff (in nm)
rvdw= 1.4   ; 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
fourier_nx  = 0
fourier_ny  = 0
fourier_nz  = 0
ewald_rtol  = 1e-5 ; relative strength of Ewald - shifted direct
potential
optimize_fft= yes ; saves computation time
; Temperature coupling is on
tcoupl  = V-rescale ; modified Berendsen thermostat
tc-grps = Non-Protein
tau_t   = 0.1   ; time constant, in ps
ref_t   = 300   ; reference temperature,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
; COM motion removal
; These options remove COM motion of the system
nstcomm = 100
comm-mode   = Linear
comm-grps   = System


Plz have a look.


Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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Re: [gmx-users] Using thermostats to create temperature gradient in system

[Justin Lemkul]

On 4/26/15 8:25 PM, Agnivo Gosai wrote:

Hello,

I am copy pasting my "mdp" file for the last step of my procedure :

Here I am not using any freeze group.

; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 5; 100 ps
dt  = 0.002 ; 2 fs
energygrps  = Protein Non-Protein
; Output control
nstxout = 10
nstvout = 10
nstlog  = 10
nstenergy   = 10
nstxtcout   = 50
; Bond parameters
continuation= yes   ; after trial 400 K
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   = 1.4   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.4   ; short-range electrostatic cutoff (in nm)
rvdw= 1.4   ; 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
fourier_nx  = 0
fourier_ny  = 0
fourier_nz  = 0
ewald_rtol  = 1e-5 ; relative strength of Ewald - shifted direct
potential
optimize_fft= yes ; saves computation time
; Temperature coupling is on
tcoupl  = V-rescale ; modified Berendsen thermostat
tc-grps = Non-Protein
tau_t   = 0.1   ; time constant, in ps
ref_t   = 300   ; reference temperature,in K


What you want is:

tc-grps = Protein Non-Protein
tau-t   = -1  0.1
ref-t   = 300 300

The ref-t for Protein is irrelevant since tau-t = -1 (as described in 
http://manual.gromacs.org/online/mdp_opt.html#tc).


-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] Using thermostats to create temperature gradient in system

[Agnivo Gosai]

Dr. Lemkul

Thanks for such an easy fix to my problem. I guess I have been doing all
sort of weird stuff since last night instead of thinking logically and
reading the relevant portion of the manual.


Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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[gmx-users] the relationship between mdp file and the force field

[Brett]

Dear All,
 
In the on-line Justin tutorial on lysozyme, the several mdp files are for the 
specific force field OPLS-AA force field. It specifically mentioned "Settings, 
particularly nonbonded interaction settings, will be different for other force 
fields".
 
Will you please introduce to me how to modify mdp files based on the difference 
of the force fields? For example, if I use force field 6, what should I modify 
based on the mdps of the lysozyme tutorial?
 
I am looking forward to getting your reply.
 
Brett
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[gmx-users] difference of calculation time between the numbers of fep-lambdas values

[nao.morishita]

Dear Gromacs Users,

I would appreciate you to give me any comments or hints about the question 
below.
What makes the calculation time much longer when I calculate a solvation free 
energy using the mdp input1 compared to the mdp input2?

Input1
Free_energy   = yes
Couple-lambda0= vdw-q
Couple-lambda1= none
Couple-intramol   = no
Init-lambda-state = 2
Fep-lambdas   = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0
Calc-lambda-neighbors = 1
Input2
Free_energy   = yes
Couple-lambda0= vdw-q
Couple-lambda1= none
Couple-intramol   = no
Init-lambda-state = 2
Fep-lambdas   = 0.0 0.1 0.2
Calc-lambda-neighbors = 1

It takes three times longer when I write down 36 lambda values compared to 3 
lambda values even if there is no difference between mdp inputs other than the 
value of fep-lambdas and it is a normal free energy calculation not like 
Hamiltonian replica exchange calculation.

Thanks in advance and best regards,

Nao

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