Re: [gmx-users] Re: Pull code with pull_geometry = cylinder generates error: Distance of pull group 1 (4.030185 nm) is larger than 0.49 times the box size (3.012310)

[David van der Spoel]

On 2012-10-08 09:05, Emma Eriksson wrote:

Thank you David for your response. Please see my reply below.

On 2012-10-04 11:50, Emma Eriksson wrote:

Dear all,

I am using the pull code in Gromacs 4.5.5 to constrain the distance in one 
direction (z) between a small molecule and a lipid bilayer. I run separate 
simulations with distances 0-4 nm constrained. I use pull_geometry = cylinder. 
The pull parameters are the following:

pull   = constraint
pull_geometry   = cylinder
pull_r1  = 1.0
pull_r0  = 1.5
pull_group0   = DMPC
pull_group1   = 2
pull_vec1  = 0 0 1
pull_init1   = x

I have previously been using the same methodology in 4.0.5 without problems. 
When i run grompp in 4.5.5 I get the following error:

Fatal error:
Distance of pull group 1 (4.030185 nm) is larger than 0.49 times the box size 
(3.012310)

The source of the first value, which should be the distance of pull group 1 is 
for me unknown. A value of ~4 is generated for all systems no matter what z 
distance is actually betwen the two groups (0-4 nm), so the value has no 
connection to the z distance between the groups. The second value is 0.5 times 
the x box length. I have read through pull.c, but I cannot find an explanation 
to why the x direction seems to be considered and not the z direction. When I 
run grompp with pull_geometry = distance or direction together with pull_dim = 
N N Y there is no problem.

As I am not sure of the source of this error when running with cylinder I do 
not know if it is only related to the check or if the following simulation 
would be affected if I uncomment the check.

Any suggestions to why this is happening and what I can do about it?
Check the other pull_XXX values in mdout.mdp
You have not specified all of them above, e.g. pull_direction?


The pull parameter section in mdout.mdp are the following:
; COM PULLING
; Pull type: no, umbrella, constraint or constant_force
pull = constraint
; Pull geometry: distance, direction, cylinder or position
pull_geometry= cylinder
; Select components for the pull vector. default: Y Y Y
pull_dim = Y Y Y
; Cylinder radius for dynamic reaction force groups (nm)
pull_r1  = 1.0
; Switch from r1 to r0 in case of dynamic reaction force
pull_r0  = 1.5
pull_constr_tol  = 1e-06
pull_start   = no
pull_nstxout = 10
pull_nstfout = 1
; Number of pull groups
pull_ngroups = 1
; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2)
pull_group0  = DMPC
pull_weights0=
pull_pbcatom0= 0
pull_group1  = 2
pull_weights1=
pull_pbcatom1= 0
pull_vec1= 0 0 1
pull_init1   = 0
pull_rate1   = 0
pull_k1  = 0
pull_kB1 = 0

I did not specify pull_dim as I understood it from the manual that this should 
not be used this for pull_geometry = cylinder (however, pull_dim will be set to 
the default Y Y Y in mdout.mdp). I specify pull_vec1 = 0 0 1, which should give 
the pull direction (z in this case). Did I misunderstand this somehow?

When I specify pull_dim = N N Y I do not get any error with grompp, but instead 
I obtain the following:

Pull group  natoms  pbc atom  distance at start reference at t=0
0  5888  2944
149 20922   3.685 0

The distance between the two groups should be 0 but the program interpret is as 
3.685, which is a value that I do not know where it comes from.

I do not know what other options I can try or what is wrong here. Do you have 
any suggestion what is going on? Thank you.


Not sure. Try replacing the cylinder with direction or so.


Emma


Thanks!

Best regards,
Emma --
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--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se--
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David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Up

[gmx-users] Nucleotide terminal problems in GORMOS96 force field

[史卜吉]

 I am going to simulate a tRNA molecule using GROMOS96 force field, which
contain some modified nucleotide.

I've build the .rtp entry for each modified residues like
this
.

But pdb2gmx prompt out such error message:

Fatal error: atom N not found in buiding block 1GUA while combining tdb and
rtp

I choose gromos43a1 force field.

I think pdb2gmx treat my nucleotide as protein, because it cap both
terminus by NH3+ and COO-.

So I redo it again, with -ter option, and choose none.

pdb2gmx say:

Fatal error: There is a dangling bond at at least one of the terminal ends.
Select a proper terminal entry.

Looks like that I should edit the terminal entry, is it correct? My .rtp
file almost exactly the same as proper nucleotide topology, the differences
exist only in the residue part.


Here is another question: why the total charge of single nucleotide
molecule is -1?


Sincerely

Daniel LIn
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Re: [gmx-users] generation of .itp file

[Erik Marklund]

Hi,

That's essentially what pdb2gmx is for.

Erik

9 okt 2012 kl. 06.50 skrev Shine A:

> sir,
> 
> I want to generate .itp from a pdb file. Is there any option in
> gromacs.
> -- 
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---
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Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html

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[gmx-users] Re: Re: Pull code with pull_geometry = cylinder generates error: Distance of pull group 1 (4.030185 nm) is larger than 0.49 times the box size (3.012310)

[Emma Eriksson]

On 2012-10-08 09:05, Emma Eriksson wrote:
> Thank you David for your response. Please see my reply below.
>
> On 2012-10-04 11:50, Emma Eriksson wrote:
>> Dear all,
>>
>> I am using the pull code in Gromacs 4.5.5 to constrain the distance in one 
>> direction (z) between a small molecule and a lipid bilayer. I run separate 
>> simulations with distances 0-4 nm constrained. I use pull_geometry = 
>> cylinder. The pull parameters are the following:
>>
>> pull   = constraint
>> pull_geometry   = cylinder
>> pull_r1  = 1.0
>> pull_r0  = 1.5
>> pull_group0   = DMPC
>> pull_group1   = 2
>> pull_vec1  = 0 0 1
>> pull_init1   = x
>>
>> I have previously been using the same methodology in 4.0.5 without problems. 
>> When i run grompp in 4.5.5 I get the following error:
>>
>> Fatal error:
>> Distance of pull group 1 (4.030185 nm) is larger than 0.49 times the box 
>> size (3.012310)
>>
>> The source of the first value, which should be the distance of pull group 1 
>> is for me unknown. A value of ~4 is generated for all systems no matter what 
>> z distance is actually betwen the two groups (0-4 nm), so the value has no 
>> connection to the z distance between the groups. The second value is 0.5 
>> times the x box length. I have read through pull.c, but I cannot find an 
>> explanation to why the x direction seems to be considered and not the z 
>> direction. When I run grompp with pull_geometry = distance or direction 
>> together with pull_dim = N N Y there is no problem.
>>
>> As I am not sure of the source of this error when running with cylinder I do 
>> not know if it is only related to the check or if the following simulation 
>> would be affected if I uncomment the check.
>>
>> Any suggestions to why this is happening and what I can do about it?
>> Check the other pull_XXX values in mdout.mdp
>> You have not specified all of them above, e.g. pull_direction?
>
> The pull parameter section in mdout.mdp are the following:
> ; COM PULLING
> ; Pull type: no, umbrella, constraint or constant_force
> pull = constraint
> ; Pull geometry: distance, direction, cylinder or position
> pull_geometry= cylinder
> ; Select components for the pull vector. default: Y Y Y
> pull_dim = Y Y Y
> ; Cylinder radius for dynamic reaction force groups (nm)
> pull_r1  = 1.0
> ; Switch from r1 to r0 in case of dynamic reaction force
> pull_r0  = 1.5
> pull_constr_tol  = 1e-06
> pull_start   = no
> pull_nstxout = 10
> pull_nstfout = 1
> ; Number of pull groups
> pull_ngroups = 1
> ; Group name, weight (default all 1), vector, init, rate (nm/ps), 
> kJ/(mol*nm^2)
> pull_group0  = DMPC
> pull_weights0=
> pull_pbcatom0= 0
> pull_group1  = 2
> pull_weights1=
> pull_pbcatom1= 0
> pull_vec1= 0 0 1
> pull_init1   = 0
> pull_rate1   = 0
> pull_k1  = 0
> pull_kB1 = 0
>
> I did not specify pull_dim as I understood it from the manual that this 
> should not be used this for pull_geometry = cylinder (however, pull_dim will 
> be set to the default Y Y Y in mdout.mdp). I specify pull_vec1 = 0 0 1, which 
> should give the pull direction (z in this case). Did I misunderstand this 
> somehow?
>
> When I specify pull_dim = N N Y I do not get any error with grompp, but 
> instead I obtain the following:
>
> Pull group  natoms  pbc atom  distance at start reference at t=0
> 0  5888  2944
> 149 20922   3.685 0
>
> The distance between the two groups should be 0 but the program interpret is 
> as 3.685, which is a value that I do not know where it comes from.
>
> I do not know what other options I can try or what is wrong here. Do you have 
> any suggestion what is going on? Thank you.
>
> Not sure. Try replacing the cylinder with direction or so.

pull_geometry = direction or distance (together with pull_dim= N N Y) works 
fine. This is why I wonder why only cylinder gives this unexpected result. I 
would prefer to use cylinder if it is possible. 

> Emma
>
>> Thanks!
>>
>> Best regards,
>> Emma --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at 
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>>
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se--
> gmx-users m

[gmx-users] Do I need to repeat my MD simulation ?

[Liu Shiyong]

 Dear all,

 I did a MD simulation (GROMACS 4.5  G53a6 force field) on
protein-peptide complex for 5ns and got an interesting conformational
change of T-loop.

However, when I rerun my script using the same input file in the same
machine, I can not observe the same or similar conformational change.
There is a significant difference between two independent run.

 What could I do for inconsistent  MD   simulation?

 Best

 Shiyong

-- 
Shiyong Liu
--
Biomolecular Physics and Modeling Group, Department of Physics,
Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
Tel：86-27-87558335-805
--
Chinese Version:
--
刘士勇
华中科技大学物理学院  生物物理模建小组
湖北省武汉市洪山区珞瑜路1037号
邮编：430074
电话：86-27-87558335-805
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[gmx-users] pull=constraint gives zero forces

[Thomas Schlesier]

But for GMX 4.0.7 there are forces in the pullf.xvg. The forces which 
arise rom the contraint the hold the two groups fixed. I use them for 
thermodynamic integration...


I use the following mdp-parameters, probably this gives you an idea what 
you might make different:

; AFM OPTIONS
pull=  constraint
pull_geometry   =  distance
pull_dim=  Y Y Y
pull_start  =  yes
pull_nstfout=  10
pull_nstxout=  50
pull_ngroups=  1
pull_group0 =  REF
pull_group1 =  ZUG
pull_rate1  = 0.000
pull_init1  = 0.000
pull_constr_tol  = 1e-06

But as Chris said, better post the complete mdp-file (probably for both 
GMX 4.0.7 and 4.5.x) so we can comment on them.


Grettings
Thomas



Am 09.10.2012 04:00, schrieb gmx-users-requ...@gromacs.org:

Please post your entire .mdp file and a snip of the output in your pullf and 
pullc files.
(Your initial post on this topic was also missing these, although the text 
reads as if you intended to include them).

I'll note that there are no forces when using constraints, so the fact that you 
get zero forces for a constrained run
is not really surprising. I guess the thing is that it doesn't work to keep 
atoms in place for you,
which we can help you with if you post more details.

Chris.

-- original message --

Following up on this post. I've tried the same runs using version 4.0.7,
which gave immediate segmentation faults. Not sure if this is a clue or a
trivial consequence of switching versions, but there it is.

Any other ideas why the pullf output just contains zeros?

Cheers,
Alex


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[gmx-users] Re: pull=constraint gives zero forces

[alex.bjorling]

Sorry - forgot to mention that before crashing, the run with all other
constraints removed produces a single line of pullf output:

0.  -812.401-4002.84482.04  1951.47 138.953 -1806.55   
-601.0072644.79 447.018 1768.6  -214.64 -199.829-2746.97   
1177.7  476.39  288.535 -559.274123.08  114.493 851.86  550.558

As Thomas Schlesier mentions here,
http://gromacs.5086.n6.nabble.com/pull-constraint-gives-zero-forces-tp5001817.html,
the pullf output apparently contains the forces necessary to enforce the
constraints.

/ Alex


alex.bjorling wrote
> Thanks guys,
> 
> Fixing the bug, recompiling and trying again results in a segfault
> like with version 4.0.7. I interpret this as GROMACS working fine, and
> suppose that there's something wrong with my input. Will continue this
> thread here and would really appreciate any ideas on how to proceed.
> 
> Before the segfault, I get a bunch of LINCS warnings, all concerning
> atoms that have other constraints in the topology. Manually replacing
> these by stiff bonds in the itp gets rid of the LINCS warnings, but
> still produces an immediate segfault.
> 
> The complete mdp follows. (Chris: previously posted via the web forum
> - it seems then you have to click the nabble link to see it).
> 
> Cheers,
> Alex
> 
> 50_constr3.mdp:
> **
> pull= constraint
> pull_geometry   = position
> pull_dim= Y Y Y
> pull_start  = yes
> pull_group0 = BB
> pull_nstxout= 1000
> pull_nstfout= 1000
> pull_ngroups= 7
> pull_constr_tol = 1e-6
> 
> pull_group1 = group1
> pull_init1  = 0.0 0.0 0.0
> pull_rate1  = 0.0 0.0 0.0
> 
> pull_group2 = group2
> pull_init2  = 0.0 0.0 0.0
> pull_rate2  = 0.0 0.0 0.0
> 
> pull_group3 = group3
> pull_init3  = 0.0 0.0 0.0
> pull_rate3  = 0.0 0.0 0.0
> 
> pull_group4 = group4
> pull_init4  = 0.0 0.0 0.0
> pull_rate4  = 0.0 0.0 0.0
> 
> pull_group5 = group5
> pull_init5  = 0.0 0.0 0.0
> pull_rate5  = 0.0 0.0 0.0
> 
> pull_group6 = group6
> pull_init6  = 0.0 0.0 0.0
> pull_rate6  = 0.0 0.0 0.0
> 
> pull_group7 = group7
> pull_init7  = 0.0 0.0 0.0
> pull_rate7  = 0.0 0.0 0.0
> 
> ;
> ; STANDARD MD INPUT OPTIONS FOR MARTINI 2.0 or 2.1
> ;
> 
> ; TIMESTEP IN MARTINI
> ; Most simulations are numerically stable
> ; with dt=40 fs, some (especially rings) require 20-30 fs.
> ; Note that time steps of 40 fs and larger may create local heating or
> ; cooling in your system. Although the use of a heat bath will globally
> ; remove this effect, it is advised to check consistency of
> ; your results for somewhat smaller time steps in the range 20-30 fs.
> ; Time steps exceeding 40 fs should not be used; time steps smaller
> ; than 20 fs are also not required.
> 
> ;define = -DPOSRES
> integrator   = md
> tinit= 0.0
> dt   = 0.02
> nsteps   = 250 ; 50 ns
> nstcomm  = 1
> comm-grps  =
> 
> nstxout  = 0
> nstvout  = 0
> nstfout  = 0
> nstlog   = 1000
> nstenergy= 100
> nstxtcout= 1000
> xtc_precision= 100
> xtc-grps =
> energygrps   = Protein
> 
> ; NEIGHBOURLIST and MARTINI
> ; Due to the use of shifted potentials, the noise generated
> ; from particles leaving/entering the neighbour list is not so large,
> ; even when large time steps are being used. In practice, once every
> ; ten steps works fine with a neighborlist cutoff that is equal to the
> ; non-bonded cutoff (1.2 nm). However, to improve energy conservation
> ; or to avoid local heating/cooling, you may increase the update frequency
> ; and/or enlarge the neighbourlist cut-off (to 1.4 nm). The latter option
> ; is computationally less expensive and leads to improved energy
> conservation
> 
> nstlist  = 10
> ns_type  = grid
> pbc  = xyz
> rlist= 1.4
> 
> ; MARTINI and NONBONDED
> ; Standard cut-off schemes are used for the non-bonded interactions
> ; in the Martini model: LJ interactions are shifted to zero in the
> ; range 0.9-1.2 nm, and electrostatic interactions in the range 0.0-1.2
> nm.
> ; The treatment of the non-bonded cut-offs is considered to be part of
> ; the force field parameterization, so we recommend not to touch these
> ; values as they will alter the overall balance of the force field.
> ; In principle you can include long range electrostatics through the use
> ; of PME, which could be more realistic in certain applications
> ; Please realize that electrostatic interactions in the Martini model are
> ; not considered to be very accurate to begin with, especially as the
> ; screening in the system is set to be uniform across the system with
> ; a screening c

Re: [gmx-users] Do I need to repeat my MD simulation ?

[Alexander Bujotzek]

Well, 5 ns is not a long time in the life of a protein-peptide complex.

I would start several (5-10?) runs with different (random) starting 
impulse to get more reliable data.


If the conformational change is connected to crossing a significant 
energy barrier, it will be a rare event... which means you have to 
sample longer in each run to have the chance to see it again.
You might use implicit solvent to see more of conformational space in 
shorther time (possibly with somewhat elevated temperature)... also see 
"simulated annealing".


Good luck and gongzuo yukuai,
Alex

Am 09.10.2012 11:17, schrieb Liu Shiyong:

  Dear all,

  I did a MD simulation (GROMACS 4.5  G53a6 force field) on
protein-peptide complex for 5ns and got an interesting conformational
change of T-loop.

However, when I rerun my script using the same input file in the same
machine, I can not observe the same or similar conformational change.
There is a significant difference between two independent run.

  What could I do for inconsistent  MD   simulation?

  Best

  Shiyong



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Re: [gmx-users] Re: pull=constraint gives zero forces

[Erik Marklund]

Hi,

Do you know there are issues with using pull=constraint on molecules that have 
constrained bonds? It's mentioned in the manual somewhere.

Erik

9 okt 2012 kl. 11.39 skrev alex.bjorling:

> Sorry - forgot to mention that before crashing, the run with all other
> constraints removed produces a single line of pullf output:
> 
> 0.  -812.401-4002.84482.04  1951.47 138.953 -1806.55  
>  
> -601.0072644.79 447.018 1768.6  -214.64 -199.829-2746.97  
>  
> 1177.7  476.39  288.535 -559.274123.08  114.493 851.86  550.558
> 
> As Thomas Schlesier mentions here,
> http://gromacs.5086.n6.nabble.com/pull-constraint-gives-zero-forces-tp5001817.html,
> the pullf output apparently contains the forces necessary to enforce the
> constraints.
> 
> / Alex
> 
> 
> alex.bjorling wrote
>> Thanks guys,
>> 
>> Fixing the bug, recompiling and trying again results in a segfault
>> like with version 4.0.7. I interpret this as GROMACS working fine, and
>> suppose that there's something wrong with my input. Will continue this
>> thread here and would really appreciate any ideas on how to proceed.
>> 
>> Before the segfault, I get a bunch of LINCS warnings, all concerning
>> atoms that have other constraints in the topology. Manually replacing
>> these by stiff bonds in the itp gets rid of the LINCS warnings, but
>> still produces an immediate segfault.
>> 
>> The complete mdp follows. (Chris: previously posted via the web forum
>> - it seems then you have to click the nabble link to see it).
>> 
>> Cheers,
>> Alex
>> 
>> 50_constr3.mdp:
>> **
>> pull= constraint
>> pull_geometry   = position
>> pull_dim= Y Y Y
>> pull_start  = yes
>> pull_group0 = BB
>> pull_nstxout= 1000
>> pull_nstfout= 1000
>> pull_ngroups= 7
>> pull_constr_tol = 1e-6
>> 
>> pull_group1 = group1
>> pull_init1  = 0.0 0.0 0.0
>> pull_rate1  = 0.0 0.0 0.0
>> 
>> pull_group2 = group2
>> pull_init2  = 0.0 0.0 0.0
>> pull_rate2  = 0.0 0.0 0.0
>> 
>> pull_group3 = group3
>> pull_init3  = 0.0 0.0 0.0
>> pull_rate3  = 0.0 0.0 0.0
>> 
>> pull_group4 = group4
>> pull_init4  = 0.0 0.0 0.0
>> pull_rate4  = 0.0 0.0 0.0
>> 
>> pull_group5 = group5
>> pull_init5  = 0.0 0.0 0.0
>> pull_rate5  = 0.0 0.0 0.0
>> 
>> pull_group6 = group6
>> pull_init6  = 0.0 0.0 0.0
>> pull_rate6  = 0.0 0.0 0.0
>> 
>> pull_group7 = group7
>> pull_init7  = 0.0 0.0 0.0
>> pull_rate7  = 0.0 0.0 0.0
>> 
>> ;
>> ; STANDARD MD INPUT OPTIONS FOR MARTINI 2.0 or 2.1
>> ;
>> 
>> ; TIMESTEP IN MARTINI
>> ; Most simulations are numerically stable
>> ; with dt=40 fs, some (especially rings) require 20-30 fs.
>> ; Note that time steps of 40 fs and larger may create local heating or
>> ; cooling in your system. Although the use of a heat bath will globally
>> ; remove this effect, it is advised to check consistency of
>> ; your results for somewhat smaller time steps in the range 20-30 fs.
>> ; Time steps exceeding 40 fs should not be used; time steps smaller
>> ; than 20 fs are also not required.
>> 
>> ;define = -DPOSRES
>> integrator   = md
>> tinit= 0.0
>> dt   = 0.02
>> nsteps   = 250 ; 50 ns
>> nstcomm  = 1
>> comm-grps =
>> 
>> nstxout  = 0
>> nstvout  = 0
>> nstfout  = 0
>> nstlog   = 1000
>> nstenergy= 100
>> nstxtcout= 1000
>> xtc_precision= 100
>> xtc-grps =
>> energygrps   = Protein
>> 
>> ; NEIGHBOURLIST and MARTINI
>> ; Due to the use of shifted potentials, the noise generated
>> ; from particles leaving/entering the neighbour list is not so large,
>> ; even when large time steps are being used. In practice, once every
>> ; ten steps works fine with a neighborlist cutoff that is equal to the
>> ; non-bonded cutoff (1.2 nm). However, to improve energy conservation
>> ; or to avoid local heating/cooling, you may increase the update frequency
>> ; and/or enlarge the neighbourlist cut-off (to 1.4 nm). The latter option
>> ; is computationally less expensive and leads to improved energy
>> conservation
>> 
>> nstlist  = 10
>> ns_type  = grid
>> pbc  = xyz
>> rlist= 1.4
>> 
>> ; MARTINI and NONBONDED
>> ; Standard cut-off schemes are used for the non-bonded interactions
>> ; in the Martini model: LJ interactions are shifted to zero in the
>> ; range 0.9-1.2 nm, and electrostatic interactions in the range 0.0-1.2
>> nm.
>> ; The treatment of the non-bonded cut-offs is considered to be part of
>> ; the force field parameterization, so we recommend not to touch these
>> ; values as they will alter the overall balance of the force field.
>> ; In principle you can include

Re: [gmx-users] Martini lipid bilayer...

[XAvier Periole]

Well ... it always depends on what you want to do but the file on the  
link you give are the official website and they should be reliable :))


On Oct 9, 2012, at 12:04 PM, rama david wrote:


Hi Gromacs friends,

I am interested in Martini force-field and application in lipid  
bilayer.

I found the lipid bilayer at

http://md.chem.rug.nl/cgmartini/index.php/downloads/example-applications/66-dppc-membrane

is it is a reliable to use it after more equilibriation ( like 500  
ns  )


or I have to build my own bilayer 

Is any other link to get the martini lipids bilayer???


With best wishes and regards,
Rama David.
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Re: [gmx-users] average velocity

[David van der Spoel]

On 2012-10-09 13:09, Dr. Vitaly Chaban wrote:

Dear All -

Is there a handy utility, which would give me an average velocity of a
given particle during the simulation?


g_traj -ov
followed by
g_analyze



Thank you!

Dr. Vitaly V. Chaban
MEMPHYS - Center for Biomembrane Physics
Department of Physics, Chemistry and Pharmacy
University of Southern Denmark
Campusvej 55, 5230 Odense M, Denmark




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Re: [gmx-users] distance between protein and ligand

[Justin Lemkul]

On 10/9/12 12:48 AM, Archana Sonawani wrote:

Hi,

I have simulated a protein-ligand complex for 5ns. I checked distance
between the important residues of protein and the ligand using g_dist. My
question is can the distance between the two groups decrease  from the
initial distance (docked complex as starting structure for simulation). I
know it may increase or may remain same at the end of the simulation.

for example: starting distance is 0.77nm and final distance is 0.8nm but
the intermediate course of simulation (around 3ns) it has decreased upto
0.65. The complex shows stability after 2ns. While the SASA between the two
groups is around 6.3 nm2  throughout the simulation which is very high.

This is very contradicting result. Is something wrong in the simulation?



I don't see anything wrong at all, though I don't understand how the SASA 
calculation connects with any of this.  That's an awfully large value for 
interfacial SASA, unless the ligand is rather large.


Distances can increase or decrease depending on the nature of the interactions 
and small conformational changes in either the ligand or the protein.


-Justin

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Blacksburg, VA
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Re: [gmx-users] Nucleotide terminal problems in GORMOS96 force field

[Justin Lemkul]

On 10/9/12 3:34 AM, 史卜吉 wrote:

  I am going to simulate a tRNA molecule using GROMOS96 force field, which
contain some modified nucleotide.



Gromos96 parameters are rather poor for nucleotides.  AMBER or CHARMM parameter 
sets are far better suited for simulations of nucleic acids.



I've build the .rtp entry for each modified residues like
this
.

But pdb2gmx prompt out such error message:

Fatal error: atom N not found in buiding block 1GUA while combining tdb and
rtp

I choose gromos43a1 force field.

I think pdb2gmx treat my nucleotide as protein, because it cap both
terminus by NH3+ and COO-.

So I redo it again, with -ter option, and choose none.

pdb2gmx say:

Fatal error: There is a dangling bond at at least one of the terminal ends.
Select a proper terminal entry.

Looks like that I should edit the terminal entry, is it correct? My .rtp
file almost exactly the same as proper nucleotide topology, the differences
exist only in the residue part.



The Gromos96 43A1 parameter set does not have entries for 5' and 3' nucleotides, 
so that's probably the root of the problem.  There is a slight error in 
residuetypes.dat, such that the residue names used by 43A1 are not identified as 
being DNA/RNA.  That should probably be fixed, but it will not solve your issue.




Here is another question: why the total charge of single nucleotide
molecule is -1?



The phosphate group of a nucleotide has a -1 charge.

-Justin

--


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Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
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[gmx-users] pull=constraint gives zero forces

[Thomas Schlesier]

For me it seems that the problem with the constraints iteration is only 
relevant if both groups are connected with contraints over the rest of 
the system.
It seems that your pull-code parameters are essentially the same like 
mine (apart from the fact that you have more groups).
In my case the system consisted of a dimer, and the pull-constraint 
acted between both monomers (which had internal constraints) and i had 
never any problems when the seperation between the two molecules was 
reasonable.


But nevertheless if the system breaks if you exchange the constraints to 
normal bonds, the is somewhere other a (probably additional) problem.

Is the system stable, when you do not use the pull-code?

Am 09.10.2012 14:26, schrieb gmx-users-requ...@gromacs.org:

Hi Erik,

Yes - I had a feeling I'd read that in the manual somewhere, which was
why I tried replacing such constraints with bonds. As I wrote above,
the LINCS warnings disappeared but the segfault remained.

Alex

2012/10/9 Erik Marklund [via GROMACS]:

>Hi,
>
>Do you know there are issues with using pull=constraint on molecules that
>have constrained bonds? It's mentioned in the manual somewhere.
>
>Erik
>
>9 okt 2012 kl. 11.39 skrev alex.bjorling:
>

>>Sorry - forgot to mention that before crashing, the run with all other
>>constraints removed produces a single line of pullf output:
>>
>>0.  -812.401-4002.84482.04  1951.47 138.953 -1806.55
>>-601.0072644.79 447.018 1768.6  -214.64 -199.829-2746.97
>>1177.7  476.39  288.535 -559.274123.08  114.493 851.86  550.558
>>
>>As Thomas Schlesier mentions here,
>>
>>http://gromacs.5086.n6.nabble.com/pull-constraint-gives-zero-forces-tp5001817.html,
>>the pullf output apparently contains the forces necessary to enforce the
>>constraints.
>>
>>/ Alex
>>
>>
>>alex.bjorling wrote

>>>Thanks guys,
>>>
>>>Fixing the bug, recompiling and trying again results in a segfault
>>>like with version 4.0.7. I interpret this as GROMACS working fine, and
>>>suppose that there's something wrong with my input. Will continue this
>>>thread here and would really appreciate any ideas on how to proceed.
>>>
>>>Before the segfault, I get a bunch of LINCS warnings, all concerning
>>>atoms that have other constraints in the topology. Manually replacing
>>>these by stiff bonds in the itp gets rid of the LINCS warnings, but
>>>still produces an immediate segfault.
>>>
>>>The complete mdp follows. (Chris: previously posted via the web forum
>>>- it seems then you have to click the nabble link to see it).
>>>
>>>Cheers,
>>>Alex
>>>
>>>50_constr3.mdp:
>>>**
>>>pull= constraint
>>>pull_geometry   = position
>>>pull_dim= Y Y Y
>>>pull_start  = yes
>>>pull_group0 = BB
>>>pull_nstxout= 1000
>>>pull_nstfout= 1000
>>>pull_ngroups= 7
>>>pull_constr_tol = 1e-6
>>>
>>>pull_group1 = group1
>>>pull_init1  = 0.0 0.0 0.0
>>>pull_rate1  = 0.0 0.0 0.0
>>>
>>>pull_group2 = group2
>>>pull_init2  = 0.0 0.0 0.0
>>>pull_rate2  = 0.0 0.0 0.0
>>>
>>>pull_group3 = group3
>>>pull_init3  = 0.0 0.0 0.0
>>>pull_rate3  = 0.0 0.0 0.0
>>>
>>>pull_group4 = group4
>>>pull_init4  = 0.0 0.0 0.0
>>>pull_rate4  = 0.0 0.0 0.0
>>>
>>>pull_group5 = group5
>>>pull_init5  = 0.0 0.0 0.0
>>>pull_rate5  = 0.0 0.0 0.0
>>>
>>>pull_group6 = group6
>>>pull_init6  = 0.0 0.0 0.0
>>>pull_rate6  = 0.0 0.0 0.0
>>>
>>>pull_group7 = group7
>>>pull_init7  = 0.0 0.0 0.0
>>>pull_rate7  = 0.0 0.0 0.0
>>>
>>>;
>>>; STANDARD MD INPUT OPTIONS FOR MARTINI 2.0 or 2.1
>>>;
>>>
>>>; TIMESTEP IN MARTINI
>>>; Most simulations are numerically stable
>>>; with dt=40 fs, some (especially rings) require 20-30 fs.
>>>; Note that time steps of 40 fs and larger may create local heating or
>>>; cooling in your system. Although the use of a heat bath will globally
>>>; remove this effect, it is advised to check consistency of
>>>; your results for somewhat smaller time steps in the range 20-30 fs.
>>>; Time steps exceeding 40 fs should not be used; time steps smaller
>>>; than 20 fs are also not required.
>>>
>>>;define = -DPOSRES
>>>integrator   = md
>>>tinit= 0.0
>>>dt   = 0.02
>>>nsteps   = 250 ; 50 ns
>>>nstcomm  = 1
>>>comm-grps =
>>>
>>>nstxout  = 0
>>>nstvout  = 0
>>>nstfout  = 0
>>>nstlog   = 1000
>>>nstenergy= 100
>>>nstxtcout= 1000
>>>xtc_precision= 100
>>>xtc-grps =
>>>energygrps   = Protein
>>>
>>>; NEIGHBOURLIST and MARTINI
>>>; Due to the use of shifted potentials, the noise generated
>>>; from particles leaving/entering the neighbour list is not so large,
>>>; even when large time steps are being used. In practice, once every
>>>; ten steps works fine

Re: [gmx-users] EM & MD

[Justin Lemkul]

On 10/9/12 9:45 AM, Ali Alizadeh wrote:

Dear All users

I ran energy minimization and mdrun for my system with

EM was a good run :

Run parameters
integrator  = steep 
dt  = 0.002
nsteps= 5
emtol =100

MD was not a good run :
integrator  = steep 


This is not MD, you're running energy minimization again.


dt  = 0.002
nsteps= 5
emtol =100


nstxout = 100   ; save coordinates every 0.2 ps
nstvout = 100   ; save velocities every 0.2 ps
nstenergy   = 100   ; save energies every 0.2 ps
nstlog  = 100   ; update log file every 0.2 ps
nstxtcout   = 100
xtc_precision   = 100

This was not converged! then increase emtol to 3000
Terminally it was converged for my mdrun,
But All of the my output files, for example hnum.xvg(g_hnum), are empty. Why?



No clue.  You haven't shown us your commands or proved that there's anything 
useful in your trajectory files (e.g. from gmxcheck) that you're analyzing.


-Justin

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Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
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Re: [gmx-users] Polarisablity of water using Gromacs

[David van der Spoel]

On 2012-10-09 14:26, Deepak Ojha wrote:

Dear Gmx_users,

I want to calculate instantaneous  polarizability of water using
GROMACS.I found there exists a water
model which polarisable in gromacs with the itp file sw.itp. Is it
possible to get the above mentioned
using the sw water model in gromacs.Are there any tools like g_hbond
which may help me get the same.

--
DeepaK Ojha
School Of Chemistry

"Selfishness is not living as one wishes to live, it is asking others
to live as one wishes to live"

The polarizability is input, the polarization is output. You may want to 
use slightly more modern models available from http://virtualchemistry.org.



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[gmx-users] Could not converge NPT constraints

[juan-manuel.castillo]

I have not much experience with Gromacs, although I have 
worked for years on molecular simulations. I am trying to 
run a NPT simulation of 1000 SPCE water molecules at 293 K 
with the opls force field. I equilibrated the system first 
during 1 ns using a velocity rescale thermostat, a 
Berendsen barostat, and a leap-frog integration method. 
Then I run a simulation using the md-vv-avek integration 
method, a Nose-Hoover thermostat, and a MTTK barostat. I 
have tried to change different parameters of the 
simulation, but after some steps I always obtain the 
following error:


Fatal error:
Could not converge NPT constraints

Anybody can help to explain what happens? I can provide 
input files if needed.

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[gmx-users] About Em and Equlibration With Lincs Algorithim

[vidhya sankar]

Dear Justin Than you for your previous Reply  

I am doing EM for My cyclic peptide using following EM. MDP

; ions.mdp - used as input into grompp to generate ions.tpr
; Parameters describing what to do, when to stop and what to save
integrator  = steep    ; Algorithm (steep = steepest descent minimization)
emtol   = 1000    ; Stop minimization when the maximum force < 1000.0 
kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps  = 5 ; Maximum number of (minimization) steps to perform
constraints = none
; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long range 
forces
ns_type = grid  ; Method to determine neighbor list (simple, grid)
rlist   = 1.4   ; Cut-off for making neighbor list (short range forces)
coulombtype = PME   ; Treatment of long range electrostatic interactions
rcoulomb    = 1.4   ; Short-range electrostatic cut-off
rvdw    = 1.4   ; Short-range Van der Waals cut-off
pbc = xyz   ; Periodic Boundary Conditions

Steepest Descents converged to machine precision in 2885 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  = -2.88282144376129e+05
Maximum force =  1.2580887753e+03 on atom 107
Norm of force =  4.38175991068554e+01

 i  Have done Five time EM using emtol  = 1000  

Every Attempt became failed Then i planned to use emtol = 1500 

In Previus Mail You Quoted the Possible emtol  = 1000 For Most of Protein in 
Water  But in My case  it is not so Because the ring is  so stained 

So  I use emtol = 1500 it is converged Successfully as follows

writing lowest energy coordinates.

Steepest Descents converged to Fmax < 1500 in 2868 steps
Potential Energy  = -2.88282144367798e+05
Maximum force =  1.31510551954873e+03 on atom 107
Norm of force =  4.39665399153860e+01


If I continue further NPT equlibration with Lincs Algorithim it shows Error aS 
follows

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 1167.301393, max 4514.205877 (between atoms 164 and 168)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    164    168  154.6    2.3463 690.8265  0.1530
    164    168  154.6    2.3463 690.8265  0.1530
    165    166  118.1    1.3451 224.6411  0.1530
    165    166  118.1    1.3451 224.6411  0.1530
    166    167   67.4    1.1731  86.2422  0.1530
    166    167   67.4    1.1731  86.2422  0.1530
    168    169  141.9    2.9836 281.9632  0.1230
    168    169  141.9    2.9836 281.9632  0.1230
  1  2   66.8    0.0735   2.3215  0.1000
  1    168   59.8    2.7313 251.2519  0.1330
  1  3  126.5    0.1241   2.3286  0.1470
    156    157   96.0    0.1464   0.3827  0.1470
    157    161  110.5    0.1604   0.4095  0.1530
    157    158   95.9    0.1523   0.3563  0.1530
    161    163   31.2    1.3955 148.8536  0.1330
    161    162   81.6    0.1293   0.6410  0.1230
    163    164  137.9    3.2852 517.7200  0.1470
    163    164  137.9    3.2852 517.7200  0.1470
  3 16   92.2    0.1534   2.8760  0.1530
  3  4   93.9    0.1528   2.8694  0.1530

Back Off! I just backed up step0b_n1.pdb to ./#step0b_n1.pdb.1#

Back Off! I just backed up step0c_n1.pdb to ./#step0c_n1.pdb.1#
Wrote pdb files with previous and current coordinates
starting mdrun 'L-22 CYCLIC PEPTIDE'
10 steps, 20.0 ps.
Warning: 1-4 interaction between 166 and 168 at distance 2.841 which is larger 
than the 1-4 table size 2.400 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size


step 0: Water molecule starting at atom 7007 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
    124    125  111.2    0.1530 297.2103  0.1530
    125    127   38.3    0.1530   0.1981  0.1530
    121    123   98.7    0.1470 1978.8023  0.1470
    119    121  139.2    0.1330 222.7882  0.1330
    119    120   35.3    0.1230   0.1629  0.1230
    106    119   33.3    0.1530   0.1945  0.1530

step 0: Water molecule starting at atom 6461 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

Back Off! I just backed up step0b_n1.pdb to ./#step0b_n1.pdb.2#



step 0: Water molecule starting at atom 2855 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

Back Off! I just backed up step0c_n1.pdb to ./#step0c_n1.pdb.2#
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates


How TO Rectify the  above errror Even I  I have Visualised the EM.gro file in 
VMD It seem to be goo

[gmx-users] Re: Distance between Centre of Mass!

[Justin Lemkul]

Please keep all Gromacs-related correspondence on the gmx-users list.  I am not 
a private tutor.  I am CC'ing this message to the list and will ask that all 
further correspondence be addressed there.


On 10/9/12 12:26 PM, Arman Mahboubi Soufiani wrote:

Dear Justin,

I have two layers of PLA and don't know the distance between their centre of
mass! Moreover, I have to change this distance to specific amount.
I have made separate indices for all the atoms on the top and bottom layer.
However, this is the step that I definitely need your direction to adjust the
correct COM between these two layers of poly(lactic acid).

I would be greatly thankful if you help me in this regard.



g_dist is the program used to measure distances.  Either you need to place the 
components in your box by specifying their locations with editconf (using 
-translate, -rotate, or -center options as needed) or use the pull code to 
adjust their positions.


-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] Could not converge NPT constraints

[Justin Lemkul]

On 10/9/12 11:31 AM, juan-manuel.casti...@mv.uni-kl.de wrote:

I have not much experience with Gromacs, although I have worked for years on
molecular simulations. I am trying to run a NPT simulation of 1000 SPCE water
molecules at 293 K with the opls force field. I equilibrated the system first
during 1 ns using a velocity rescale thermostat, a Berendsen barostat, and a
leap-frog integration method. Then I run a simulation using the md-vv-avek
integration method, a Nose-Hoover thermostat, and a MTTK barostat. I have tried
to change different parameters of the simulation, but after some steps I always
obtain the following error:

Fatal error:
Could not converge NPT constraints

Anybody can help to explain what happens? I can provide input files if needed.


An .mdp file would be helpful.

The failure is coming from the done_iterating() function in 
src/mdlib/iteratedconstraints.c, and there are actually quite extensive comments 
in the code about what the function is doing.  Perhaps you can deduce some 
useful information from the description there.


-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] single precision to double precision version

[Justin Lemkul]

On 10/9/12 12:21 PM, Ali Alizadeh wrote:

Dear All users

How to convert my single precision version of gromacs to double precision?

Is it possible?



You don't; you re-install Gromacs with the desired precision.  Note that single- 
and double-precision installations can exist side-by-side with proper suffixes 
(default _d) on the executables and libraries.



Can i do it by apt get command in ubuntu version?



It looks to me like the only version available is single-precision but perhaps 
someone else who uses them regularly can tell.  I do all my installations from 
source.


-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] About Em and Equlibration With Lincs Algorithim

[Justin Lemkul]

On 10/9/12 12:38 PM, vidhya sankar wrote:

Dear Justin Than you for your previous Reply

I am doing EM for My cyclic peptide using following EM. MDP

; ions.mdp - used as input into grompp to generate ions.tpr
; Parameters describing what to do, when to stop and what to save
integrator  = steep; Algorithm (steep = steepest descent minimization)
emtol   = 1000; Stop minimization when the maximum force < 1000.0 
kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps  = 5 ; Maximum number of (minimization) steps to perform
constraints = none
; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long range 
forces
ns_type = grid  ; Method to determine neighbor list (simple, grid)
rlist   = 1.4   ; Cut-off for making neighbor list (short range forces)
coulombtype = PME   ; Treatment of long range electrostatic interactions
rcoulomb= 1.4   ; Short-range electrostatic cut-off
rvdw= 1.4   ; Short-range Van der Waals cut-off
pbc = xyz   ; Periodic Boundary Conditions

Steepest Descents converged to machine precision in 2885 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  = -2.88282144376129e+05
Maximum force =  1.2580887753e+03 on atom 107
Norm of force =  4.38175991068554e+01

  i  Have done Five time EM using emtol  = 1000

Every Attempt became failed Then i planned to use emtol = 1500

In Previus Mail You Quoted the Possible emtol  = 1000 For Most of Protein in 
Water  But in My case  it is not so Because the ring is  so stained

So  I use emtol = 1500 it is converged Successfully as follows

writing lowest energy coordinates.

Steepest Descents converged to Fmax < 1500 in 2868 steps
Potential Energy  = -2.88282144367798e+05
Maximum force =  1.31510551954873e+03 on atom 107
Norm of force =  4.39665399153860e+01


If I continue further NPT equlibration with Lincs Algorithim it shows Error aS 
follows

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 1167.301393, max 4514.205877 (between atoms 164 and 168)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
 164168  154.62.3463 690.8265  0.1530
 164168  154.62.3463 690.8265  0.1530
 165166  118.11.3451 224.6411  0.1530
 165166  118.11.3451 224.6411  0.1530
 166167   67.41.1731  86.2422  0.1530
 166167   67.41.1731  86.2422  0.1530
 168169  141.92.9836 281.9632  0.1230
 168169  141.92.9836 281.9632  0.1230
   1  2   66.80.0735   2.3215  0.1000
   1168   59.82.7313 251.2519  0.1330
   1  3  126.50.1241   2.3286  0.1470
 156157   96.00.1464   0.3827  0.1470
 157161  110.50.1604   0.4095  0.1530
 157158   95.90.1523   0.3563  0.1530
 161163   31.21.3955 148.8536  0.1330
 161162   81.60.1293   0.6410  0.1230
 163164  137.93.2852 517.7200  0.1470
 163164  137.93.2852 517.7200  0.1470
   3 16   92.20.1534   2.8760  0.1530
   3  4   93.90.1528   2.8694  0.1530

Back Off! I just backed up step0b_n1.pdb to ./#step0b_n1.pdb.1#

Back Off! I just backed up step0c_n1.pdb to ./#step0c_n1.pdb.1#
Wrote pdb files with previous and current coordinates
starting mdrun 'L-22 CYCLIC PEPTIDE'
10 steps, 20.0 ps.
Warning: 1-4 interaction between 166 and 168 at distance 2.841 which is larger 
than the 1-4 table size 2.400 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size


step 0: Water molecule starting at atom 7007 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
 124125  111.20.1530 297.2103  0.1530
 125127   38.30.1530   0.1981  0.1530
 121123   98.70.1470 1978.8023  0.1470
 119121  139.20.1330 222.7882  0.1330
 119120   35.30.1230   0.1629  0.1230
 106119   33.30.1530   0.1945  0.1530

step 0: Water molecule starting at atom 6461 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

Back Off! I just backed up step0b_n1.pdb to ./#step0b_n1.pdb.2#



step 0: Water molecule starting at atom 2855 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

Back Off! I just backed up step0c_n1.pdb to ./#step0c_n1.pdb.2#
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates


How TO Rectify the  above errror

[gmx-users] RB parameters for the OPLSAA force field.

[Elie M]

Dear all,
Does anyone know where I can find reference of how to calculate the RB 
parameters (C0-C5) for proper dihedrals? I have got some undefined dihedrals in 
my top file and I am not sure where to start. What kind of information do i 
need to calculate those parameters? any package that does that?


Thanks

Elie  --
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Re: [gmx-users] distance between protein and ligand

[Liu Shiyong]

Hi,

Did u repeat your MD simulation of your docked complex ?

I also asked the similar question. Alex replied :" I would start
several (5-10?) runs with different (random) starting impulse to get
more reliable data."

Best

Shiyong


On Tue, Oct 9, 2012 at 12:48 PM, Archana Sonawani  wrote:
> Hi,
>
> I have simulated a protein-ligand complex for 5ns. I checked distance
> between the important residues of protein and the ligand using g_dist. My
> question is can the distance between the two groups decrease  from the
> initial distance (docked complex as starting structure for simulation). I
> know it may increase or may remain same at the end of the simulation.
>
> for example: starting distance is 0.77nm and final distance is 0.8nm but
> the intermediate course of simulation (around 3ns) it has decreased upto
> 0.65. The complex shows stability after 2ns. While the SASA between the two
> groups is around 6.3 nm2  throughout the simulation which is very high.
>
> This is very contradicting result. Is something wrong in the simulation?
>
> Thanks in advance.
>
> --
> Archana Sonawani-Jagtap
> Junior Research Fellow,
> Biomedical Informatics Centre,
> NIRRH (ICMR), Parel
> Mumbai, India.
> 9960791339
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at 
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-- 
Shiyong Liu
--
Biomolecular Physics and Modeling Group, Department of Physics,
Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
Tel：86-27-87558335-805
--
Chinese Version:
--
刘士勇
华中科技大学物理学院  生物物理模建小组
湖北省武汉市洪山区珞瑜路1037号
邮编：430074
电话：86-27-87558335-805
---
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Re: [gmx-users] Interaction study for peptide-receptor..

[Liu Shiyong]

Hi,

Your expectation from MD is too much than reality.

Peptide design is an open problem. Lots of elegant protocols are
available. However, to my understanding, the core problem is still
about protein-peptide docking and scoring. MD simulation only helps on
some special cases. It is impossible that MD simulation is used to for
screening peptide library.

Best

Shiyong


On Thu, Oct 4, 2012 at 9:16 PM, rama david  wrote:
> Thank you  for reply,
>  I read the recently published article in Biochemistry.
> They worked on the same receptor that I am working.
> ( as I mention in my previous mail)
> They used NAMD software and I am using gromacs.
> They sliced the  receptor binding site and used the the solid support
> to the binding site and did simulation.
>So if I freeze  the group is it will ok ??
> Is it possible in gromacs to fix the residue on solid immobilized surface.
> If it is how to do it??
>
> my question is How to decide which group are remove and which group should
> keep in simulation.
>
> thank you in advance
> Thank you for giving your valuable time and advice to me.
>
> With best wishes and regards,
> Rama david
>
>
>
>
>
>
> On Thu, Oct 4, 2012 at 6:11 PM, Thomas Evangelidis wrote:
>
>> I don't think AutoDock and Vina are suitable for peptide docking. I would
>> first try the FlexPepDocking module of Rosetta which does ab initio folding
>> of the peptide on the receptor, while moving the side-chains of the protein
>> but leaves its backbone intact. Rosetta implements a knowledge-based
>> scoring, which has been specifically designed for this task and is as fast
>> as Vina or AutoDock.
>>
>> I would first do that and if I wouldn't get any reasonable results then I
>> would move to MD starting from the top scored protein-peptide complexes
>> created by Rosetta.
>>
>> Thomas
>>
>>
>> On 4 October 2012 15:08, rama david  wrote:
>>
>> > Hi francesco,
>> >
>> > Thank you For reply.
>> > I did docking but the result are not so impressive.
>> > I used vina and autodock.
>> > I also did virtual screening in autodock but the result are not upto the
>> > mark.
>> >
>> > Is the freezing of group can affect my system?? How much efficiency I get
>> > by these work??
>> > As these group are going to freeze in four simulation so if it affect one
>> > ligand it  affect other
>> > ligand also.
>> >
>> > I read article that did the work like me ,
>> > they sliced the binding residues and  used the inert solid sphere to
>> > support binding residues
>> > instead of the freezing group other group.
>> >
>> > I think both way should have same effect..Am I right or wrong??
>> >
>> > If you have any other way please suggest it..
>> >
>> > With best wishes and regards
>> > Rama david
>> >
>> >
>> > On Thu, Oct 4, 2012 at 5:07 PM, francesco oteri
>> > wrote:
>> >
>> > > Hi,
>> > > as far as I know, freezing just set velocities to 0 so you gain nothing
>> > > freezing atoms.
>> > >
>> > > By the way, have you tried docking? It takes into account multiple
>> > > conformation and
>> > > orientation of the peptide and, depending upon the implemented
>> algorithm,
>> > > also
>> > > protein sidechain orientation.
>> > >
>> > > Francesco
>> > >
>> > >
>> > > 2012/10/4 rama david 
>> > >
>> > > > thank you Justin for reply.
>> > > >
>> > > > I dont know about long range interactions.
>> > > > But as I freeze the group I think it will improve my computational
>> > speed.
>> > > > So is there any way to find out or decide which group should be
>> > > > freeze, and which group should affect my interaction most probably??
>> > > >
>> > > > Should I do Essential Dynamics ??? or Principle component analysis
>> ???
>> > > >
>> > > > Would you suggest me any general protocol for such work??
>> > > >
>> > > > Thank you in Advance
>> > > >
>> > > >
>> > > > With Best Wishes and regards.
>> > > > Rama David
>> > > >
>> > > > On Thu, Oct 4, 2012 at 3:57 PM, Justin Lemkul 
>> wrote:
>> > > >
>> > > > >
>> > > > >
>> > > > > On 10/4/12 2:01 AM, rama david wrote:
>> > > > >
>> > > > >> Hi gromacs Friends,
>> > > > >>  I want to do peptide-receptor ( Protein) interaction
>> > > > >> study.Receptor consist a single chain.
>> > > > >> Peptide is made up  of  4 amino acids. I know the interaction
>> > pattern
>> > > of
>> > > > >> peptide and receptor.
>> > > > >> I plan to mutate single residue each at a time and  run 4
>> > simulation .
>> > > > >> So I will have the 4 different simulation that contain the mutated
>> > > > >> residues
>> > > > >> and the wild one.
>> > > > >>
>> > > > >>
>> > > > >> Then afterward from the interaction energy I want to select the
>> > > peptide
>> > > > >> which is showing
>> > > > >> stronger interaction than others.
>> > > > >>
>> > > > >> As  mention I know the binding site, If I freeze the remaining
>> > portion
>> > > > in
>> > > > >> receptor
>> > > > >> that not involved in binding , Is it going to affect my screening
>> > > > process
>> > > > >> ???
>> > > > >>
>> > > >

Re: [gmx-users] Interaction study for peptide-receptor..

[Justin Lemkul]

On 10/9/12 8:43 PM, Liu Shiyong wrote:

Hi,

Your expectation from MD is too much than reality.

Peptide design is an open problem. Lots of elegant protocols are
available. However, to my understanding, the core problem is still
about protein-peptide docking and scoring. MD simulation only helps on
some special cases. It is impossible that MD simulation is used to for
screening peptide library.



I would hardly call 4 different mutants a library.  Plenty of methods exist to 
enhance the sampling of such systems and have been used to great effect. 
Computationally expensive to pull off properly?  Yes.  Impossible?  In this 
case, I would say no.


-Justin



On Thu, Oct 4, 2012 at 9:16 PM, rama david  wrote:

Thank you  for reply,
  I read the recently published article in Biochemistry.
They worked on the same receptor that I am working.
( as I mention in my previous mail)
They used NAMD software and I am using gromacs.
They sliced the  receptor binding site and used the the solid support
to the binding site and did simulation.
So if I freeze  the group is it will ok ??
Is it possible in gromacs to fix the residue on solid immobilized surface.
If it is how to do it??

my question is How to decide which group are remove and which group should
keep in simulation.

thank you in advance
Thank you for giving your valuable time and advice to me.

With best wishes and regards,
Rama david






On Thu, Oct 4, 2012 at 6:11 PM, Thomas Evangelidis wrote:


I don't think AutoDock and Vina are suitable for peptide docking. I would
first try the FlexPepDocking module of Rosetta which does ab initio folding
of the peptide on the receptor, while moving the side-chains of the protein
but leaves its backbone intact. Rosetta implements a knowledge-based
scoring, which has been specifically designed for this task and is as fast
as Vina or AutoDock.

I would first do that and if I wouldn't get any reasonable results then I
would move to MD starting from the top scored protein-peptide complexes
created by Rosetta.

Thomas


On 4 October 2012 15:08, rama david  wrote:


Hi francesco,

Thank you For reply.
I did docking but the result are not so impressive.
I used vina and autodock.
I also did virtual screening in autodock but the result are not upto the
mark.

Is the freezing of group can affect my system?? How much efficiency I get
by these work??
As these group are going to freeze in four simulation so if it affect one
ligand it  affect other
ligand also.

I read article that did the work like me ,
they sliced the binding residues and  used the inert solid sphere to
support binding residues
instead of the freezing group other group.

I think both way should have same effect..Am I right or wrong??

If you have any other way please suggest it..

With best wishes and regards
Rama david


On Thu, Oct 4, 2012 at 5:07 PM, francesco oteri
wrote:


Hi,
as far as I know, freezing just set velocities to 0 so you gain nothing
freezing atoms.

By the way, have you tried docking? It takes into account multiple
conformation and
orientation of the peptide and, depending upon the implemented

algorithm,

also
protein sidechain orientation.

Francesco


2012/10/4 rama david 


thank you Justin for reply.

I dont know about long range interactions.
But as I freeze the group I think it will improve my computational

speed.

So is there any way to find out or decide which group should be
freeze, and which group should affect my interaction most probably??

Should I do Essential Dynamics ??? or Principle component analysis

???


Would you suggest me any general protocol for such work??

Thank you in Advance


With Best Wishes and regards.
Rama David

On Thu, Oct 4, 2012 at 3:57 PM, Justin Lemkul 

wrote:





On 10/4/12 2:01 AM, rama david wrote:


Hi gromacs Friends,
  I want to do peptide-receptor ( Protein) interaction
study.Receptor consist a single chain.
Peptide is made up  of  4 amino acids. I know the interaction

pattern

of

peptide and receptor.
I plan to mutate single residue each at a time and  run 4

simulation .

So I will have the 4 different simulation that contain the mutated
residues
and the wild one.


Then afterward from the interaction energy I want to select the

peptide

which is showing
stronger interaction than others.

As  mention I know the binding site, If I freeze the remaining

portion

in

receptor
that not involved in binding , Is it going to affect my screening

process

???



Potentially.  Do you know that the binding interactions and the

mutations

will only perturb local residues?  Do you know that there are no

long-range

motions to be considered?

I think you gain very little by freezing portions of the system,

and

risk

more than you gain.

-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/Pag

Re: [gmx-users] Interaction study for peptide-receptor..

[Liu Shiyong]

Justin,

 Single mutation for four residue. The number of mutants is 4x19=76
Of course , that is a tiny peptide library.


Best

Shiyong

On Wed, Oct 10, 2012 at 9:06 AM, Justin Lemkul  wrote:
>
>
> On 10/9/12 8:43 PM, Liu Shiyong wrote:
>>
>> Hi,
>>
>> Your expectation from MD is too much than reality.
>>
>> Peptide design is an open problem. Lots of elegant protocols are
>> available. However, to my understanding, the core problem is still
>> about protein-peptide docking and scoring. MD simulation only helps on
>> some special cases. It is impossible that MD simulation is used to for
>> screening peptide library.
>>
>
> I would hardly call 4 different mutants a library.  Plenty of methods exist
> to enhance the sampling of such systems and have been used to great effect.
> Computationally expensive to pull off properly?  Yes.  Impossible?  In this
> case, I would say no.
>
> -Justin
>
>
>>
>> On Thu, Oct 4, 2012 at 9:16 PM, rama david 
>> wrote:
>>>
>>> Thank you  for reply,
>>>   I read the recently published article in Biochemistry.
>>> They worked on the same receptor that I am working.
>>> ( as I mention in my previous mail)
>>> They used NAMD software and I am using gromacs.
>>> They sliced the  receptor binding site and used the the solid support
>>> to the binding site and did simulation.
>>> So if I freeze  the group is it will ok ??
>>> Is it possible in gromacs to fix the residue on solid immobilized
>>> surface.
>>> If it is how to do it??
>>>
>>> my question is How to decide which group are remove and which group
>>> should
>>> keep in simulation.
>>>
>>> thank you in advance
>>> Thank you for giving your valuable time and advice to me.
>>>
>>> With best wishes and regards,
>>> Rama david
>>>
>>>
>>>
>>>
>>>
>>>
>>> On Thu, Oct 4, 2012 at 6:11 PM, Thomas Evangelidis
>>> wrote:
>>>
 I don't think AutoDock and Vina are suitable for peptide docking. I
 would
 first try the FlexPepDocking module of Rosetta which does ab initio
 folding
 of the peptide on the receptor, while moving the side-chains of the
 protein
 but leaves its backbone intact. Rosetta implements a knowledge-based
 scoring, which has been specifically designed for this task and is as
 fast
 as Vina or AutoDock.

 I would first do that and if I wouldn't get any reasonable results then
 I
 would move to MD starting from the top scored protein-peptide complexes
 created by Rosetta.

 Thomas


 On 4 October 2012 15:08, rama david  wrote:

> Hi francesco,
>
> Thank you For reply.
> I did docking but the result are not so impressive.
> I used vina and autodock.
> I also did virtual screening in autodock but the result are not upto
> the
> mark.
>
> Is the freezing of group can affect my system?? How much efficiency I
> get
> by these work??
> As these group are going to freeze in four simulation so if it affect
> one
> ligand it  affect other
> ligand also.
>
> I read article that did the work like me ,
> they sliced the binding residues and  used the inert solid sphere to
> support binding residues
> instead of the freezing group other group.
>
> I think both way should have same effect..Am I right or wrong??
>
> If you have any other way please suggest it..
>
> With best wishes and regards
> Rama david
>
>
> On Thu, Oct 4, 2012 at 5:07 PM, francesco oteri
> wrote:
>
>> Hi,
>> as far as I know, freezing just set velocities to 0 so you gain
>> nothing
>> freezing atoms.
>>
>> By the way, have you tried docking? It takes into account multiple
>> conformation and
>> orientation of the peptide and, depending upon the implemented

 algorithm,
>>
>> also
>> protein sidechain orientation.
>>
>> Francesco
>>
>>
>> 2012/10/4 rama david 
>>
>>> thank you Justin for reply.
>>>
>>> I dont know about long range interactions.
>>> But as I freeze the group I think it will improve my computational
>
> speed.
>>>
>>> So is there any way to find out or decide which group should be
>>> freeze, and which group should affect my interaction most probably??
>>>
>>> Should I do Essential Dynamics ??? or Principle component analysis

 ???
>>>
>>>
>>> Would you suggest me any general protocol for such work??
>>>
>>> Thank you in Advance
>>>
>>>
>>> With Best Wishes and regards.
>>> Rama David
>>>
>>> On Thu, Oct 4, 2012 at 3:57 PM, Justin Lemkul 

 wrote:
>>>
>>>


 On 10/4/12 2:01 AM, rama david wrote:

> Hi gromacs Friends,
>   I want to do peptide-receptor ( Protein) interaction
> study.Receptor consist a single chain.
> Peptide is made up  of  4 amino acids. I know

Re: [gmx-users] Interaction study for peptide-receptor..

[Justin Lemkul]

On 10/9/12 9:17 PM, Liu Shiyong wrote:

Justin,

  Single mutation for four residue. The number of mutants is 4x19=76
Of course , that is a tiny peptide library.



Of course one can design many different mutants with a 4-residue peptide (far 
more than 76 in fact, considering all possible combinations of all 20 amino 
acids), but I do not believe that is the intent of the OP here.  Referring to 
the original post:


http://lists.gromacs.org/pipermail/gmx-users/2012-October/075182.html

It seems that 4 total simulations are intended (perhaps 4 simulations with 
replicates).


-Justin


On Wed, Oct 10, 2012 at 9:06 AM, Justin Lemkul  wrote:



On 10/9/12 8:43 PM, Liu Shiyong wrote:


Hi,

Your expectation from MD is too much than reality.

Peptide design is an open problem. Lots of elegant protocols are
available. However, to my understanding, the core problem is still
about protein-peptide docking and scoring. MD simulation only helps on
some special cases. It is impossible that MD simulation is used to for
screening peptide library.



I would hardly call 4 different mutants a library.  Plenty of methods exist
to enhance the sampling of such systems and have been used to great effect.
Computationally expensive to pull off properly?  Yes.  Impossible?  In this
case, I would say no.

-Justin




On Thu, Oct 4, 2012 at 9:16 PM, rama david 
wrote:


Thank you  for reply,
   I read the recently published article in Biochemistry.
They worked on the same receptor that I am working.
( as I mention in my previous mail)
They used NAMD software and I am using gromacs.
They sliced the  receptor binding site and used the the solid support
to the binding site and did simulation.
 So if I freeze  the group is it will ok ??
Is it possible in gromacs to fix the residue on solid immobilized
surface.
If it is how to do it??

my question is How to decide which group are remove and which group
should
keep in simulation.

thank you in advance
Thank you for giving your valuable time and advice to me.

With best wishes and regards,
Rama david






On Thu, Oct 4, 2012 at 6:11 PM, Thomas Evangelidis
wrote:


I don't think AutoDock and Vina are suitable for peptide docking. I
would
first try the FlexPepDocking module of Rosetta which does ab initio
folding
of the peptide on the receptor, while moving the side-chains of the
protein
but leaves its backbone intact. Rosetta implements a knowledge-based
scoring, which has been specifically designed for this task and is as
fast
as Vina or AutoDock.

I would first do that and if I wouldn't get any reasonable results then
I
would move to MD starting from the top scored protein-peptide complexes
created by Rosetta.

Thomas


On 4 October 2012 15:08, rama david  wrote:


Hi francesco,

Thank you For reply.
I did docking but the result are not so impressive.
I used vina and autodock.
I also did virtual screening in autodock but the result are not upto
the
mark.

Is the freezing of group can affect my system?? How much efficiency I
get
by these work??
As these group are going to freeze in four simulation so if it affect
one
ligand it  affect other
ligand also.

I read article that did the work like me ,
they sliced the binding residues and  used the inert solid sphere to
support binding residues
instead of the freezing group other group.

I think both way should have same effect..Am I right or wrong??

If you have any other way please suggest it..

With best wishes and regards
Rama david


On Thu, Oct 4, 2012 at 5:07 PM, francesco oteri
wrote:


Hi,
as far as I know, freezing just set velocities to 0 so you gain
nothing
freezing atoms.

By the way, have you tried docking? It takes into account multiple
conformation and
orientation of the peptide and, depending upon the implemented


algorithm,


also
protein sidechain orientation.

Francesco


2012/10/4 rama david 


thank you Justin for reply.

I dont know about long range interactions.
But as I freeze the group I think it will improve my computational


speed.


So is there any way to find out or decide which group should be
freeze, and which group should affect my interaction most probably??

Should I do Essential Dynamics ??? or Principle component analysis


???



Would you suggest me any general protocol for such work??

Thank you in Advance


With Best Wishes and regards.
Rama David

On Thu, Oct 4, 2012 at 3:57 PM, Justin Lemkul 


wrote:






On 10/4/12 2:01 AM, rama david wrote:


Hi gromacs Friends,
   I want to do peptide-receptor ( Protein) interaction
study.Receptor consist a single chain.
Peptide is made up  of  4 amino acids. I know the interaction


pattern


of


peptide and receptor.
I plan to mutate single residue each at a time and  run 4


simulation .


So I will have the 4 different simulation that contain the mutated
residues
and the wild one.


Then afterward from the interaction energy I want to select the


peptide


which is showing
stronger interaction than others.

As  mention

Re: [gmx-users] single precision to double precision version

[Oliver Stueker]

On Tue, Oct 9, 2012 at 12:07 PM, Justin Lemkul  wrote:
>
>
> On 10/9/12 12:21 PM, Ali Alizadeh wrote:
>>
>> Dear All users
>>
>> How to convert my single precision version of gromacs to double precision?
>>
>> Is it possible?
>>
>
> You don't; you re-install Gromacs with the desired precision.  Note that
> single- and double-precision installations can exist side-by-side with
> proper suffixes (default _d) on the executables and libraries.
>
>
>> Can i do it by apt get command in ubuntu version?
>>
>
> It looks to me like the only version available is single-precision but
> perhaps someone else who uses them regularly can tell.  I do all my
> installations from source.
>
> -Justin
>

The gromacs packages that come with Ubuntu contain both single and
double-precision binaries, with the latter ones having the usual _d suffix.

I have checked that on Ubuntu 10.04 Lucid Lynx (gromacs 4.0.7) and
Ubuntu 12.04 Precise Pangolin (gromacs 4.5.5).


Oliver

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Re: [gmx-users] Interaction study for peptide-receptor..

[rama david]

Hi,

Yes it is possible to screen peptides as ligand.

But for these following information is needed

1.  Binding site of peptide and ligand
 2. Which residues in peptide are important for binding.

After you simply do the mutation on the desired peptide.Performed the MD
upto 50 ns

Find the interaction energy.

As the MD need a lot of time , you can´t use it for the large library.
I plan to do only 5 simulation.


With best wishes and regards.
Rama david




On Wed, Oct 10, 2012 at 6:54 AM, Justin Lemkul  wrote:

>
>
> On 10/9/12 9:17 PM, Liu Shiyong wrote:
>
>> Justin,
>>
>>   Single mutation for four residue. The number of mutants is 4x19=76
>> Of course , that is a tiny peptide library.
>>
>>
> Of course one can design many different mutants with a 4-residue peptide
> (far more than 76 in fact, considering all possible combinations of all 20
> amino acids), but I do not believe that is the intent of the OP here.
>  Referring to the original post:
>
> http://lists.gromacs.org/**pipermail/gmx-users/2012-**October/075182.html
>
> It seems that 4 total simulations are intended (perhaps 4 simulations with
> replicates).
>
> -Justin
>
>
>  On Wed, Oct 10, 2012 at 9:06 AM, Justin Lemkul  wrote:
>>
>>>
>>>
>>> On 10/9/12 8:43 PM, Liu Shiyong wrote:
>>>

 Hi,

 Your expectation from MD is too much than reality.

 Peptide design is an open problem. Lots of elegant protocols are
 available. However, to my understanding, the core problem is still
 about protein-peptide docking and scoring. MD simulation only helps on
 some special cases. It is impossible that MD simulation is used to for
 screening peptide library.


>>> I would hardly call 4 different mutants a library.  Plenty of methods
>>> exist
>>> to enhance the sampling of such systems and have been used to great
>>> effect.
>>> Computationally expensive to pull off properly?  Yes.  Impossible?  In
>>> this
>>> case, I would say no.
>>>
>>> -Justin
>>>
>>>
>>>
 On Thu, Oct 4, 2012 at 9:16 PM, rama david 
 wrote:

>
> Thank you  for reply,
>I read the recently published article in Biochemistry.
> They worked on the same receptor that I am working.
> ( as I mention in my previous mail)
> They used NAMD software and I am using gromacs.
> They sliced the  receptor binding site and used the the solid support
> to the binding site and did simulation.
>  So if I freeze  the group is it will ok ??
> Is it possible in gromacs to fix the residue on solid immobilized
> surface.
> If it is how to do it??
>
> my question is How to decide which group are remove and which group
> should
> keep in simulation.
>
> thank you in advance
> Thank you for giving your valuable time and advice to me.
>
> With best wishes and regards,
> Rama david
>
>
>
>
>
>
> On Thu, Oct 4, 2012 at 6:11 PM, Thomas Evangelidis
> wrote:
>
>  I don't think AutoDock and Vina are suitable for peptide docking. I
>> would
>> first try the FlexPepDocking module of Rosetta which does ab initio
>> folding
>> of the peptide on the receptor, while moving the side-chains of the
>> protein
>> but leaves its backbone intact. Rosetta implements a knowledge-based
>> scoring, which has been specifically designed for this task and is as
>> fast
>> as Vina or AutoDock.
>>
>> I would first do that and if I wouldn't get any reasonable results
>> then
>> I
>> would move to MD starting from the top scored protein-peptide
>> complexes
>> created by Rosetta.
>>
>> Thomas
>>
>>
>> On 4 October 2012 15:08, rama david  wrote:
>>
>>  Hi francesco,
>>>
>>> Thank you For reply.
>>> I did docking but the result are not so impressive.
>>> I used vina and autodock.
>>> I also did virtual screening in autodock but the result are not upto
>>> the
>>> mark.
>>>
>>> Is the freezing of group can affect my system?? How much efficiency I
>>> get
>>> by these work??
>>> As these group are going to freeze in four simulation so if it affect
>>> one
>>> ligand it  affect other
>>> ligand also.
>>>
>>> I read article that did the work like me ,
>>> they sliced the binding residues and  used the inert solid sphere to
>>> support binding residues
>>> instead of the freezing group other group.
>>>
>>> I think both way should have same effect..Am I right or wrong??
>>>
>>> If you have any other way please suggest it..
>>>
>>> With best wishes and regards
>>> Rama david
>>>
>>>
>>> On Thu, Oct 4, 2012 at 5:07 PM, francesco oteri
>>> **wrote:
>>>
>>>  Hi,
 as far as I know, freezing just set velocities to 0 so you gain
 nothing
>>>

Re: [gmx-users] distance between protein and ligand

[Archana Sonawani]

Hi  Liu Shiyong,

No, I didn't repeat any simulation. My intention is to compare two large
compounds with our designed molecule which is comparatively smaller.

On Wed, Oct 10, 2012 at 6:01 AM, Liu Shiyong  wrote:

> Hi,
>
> Did u repeat your MD simulation of your docked complex ?
>
> I also asked the similar question. Alex replied :" I would start
> several (5-10?) runs with different (random) starting impulse to get
> more reliable data."
>
> Best
>
> Shiyong
>
>
> On Tue, Oct 9, 2012 at 12:48 PM, Archana Sonawani 
> wrote:
> > Hi,
> >
> > I have simulated a protein-ligand complex for 5ns. I checked distance
> > between the important residues of protein and the ligand using g_dist. My
> > question is can the distance between the two groups decrease  from the
> > initial distance (docked complex as starting structure for simulation). I
> > know it may increase or may remain same at the end of the simulation.
> >
> > for example: starting distance is 0.77nm and final distance is 0.8nm but
> > the intermediate course of simulation (around 3ns) it has decreased upto
> > 0.65. The complex shows stability after 2ns. While the SASA between the
> two
> > groups is around 6.3 nm2  throughout the simulation which is very high.
> >
> > This is very contradicting result. Is something wrong in the simulation?
> >
> > Thanks in advance.
> >
> > --
> > Archana Sonawani-Jagtap
> > Junior Research Fellow,
> > Biomedical Informatics Centre,
> > NIRRH (ICMR), Parel
> > Mumbai, India.
> > 9960791339
> > --
> > gmx-users mailing listgmx-users@gromacs.org
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>
>
>
> --
> Shiyong Liu
> --
> Biomolecular Physics and Modeling Group, Department of Physics,
> Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
> Tel：86-27-87558335-805
> --
> Chinese Version:
> --
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-- 
Archana Sonawani-Jagtap
Junior Research Fellow,
Biomedical Informatics Centre,
NIRRH (ICMR), Parel
Mumbai, India.
9960791339
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[gmx-users] TPI run

[rikhiag]

Dear users,

I want to run TPI of water in a binary mixture of water DMSO system. My
question is, how to add the extra water or extra DMSO molecule, or
precisely, how to get the NEW set of coordinates for one water OR one DMSO
molecule?

I will appreciate your reply.

Rikg



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