[gmx-users] Questions concerning Gromacs

[Thomas Koller]

Hello,

I have some questions concerning the implementation in Gromacs:

1) I want to model a rigid anion of an IL (fixed bonds and angles). The cation 
is flexible. How can I do that without using constraint types? With LINCS or 
SHAKE, I can only fix, for instance, bonds with H atoms or all atoms. Can I use 
high values for the force constants?

2) When implementing improper dihedrals, I write the sequences of the four 
atoms in the [dihedraltypes] and then fix them in the [dihedral] directive. But 
I always get the error that the impropers are not defined in the default. What 
is my problem? I use function type 2. The sequence of impropers is: center atom 
- neighbor atom - neighbor atom- neighbor atom,
as I saw in the manual.

3) For function type 1 of the dihedrals, I implement the equilibrium angle, the 
force constant and the multiplicity (one value for all kinds). What should I do 
if I have, for instance, three equilibrium angles, different for the 
multiplicities (n=1,2,3). How can I implement that in the top file?

Thanks for your efforts!
Regards,
Thomas
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Re: [gmx-users] Re:Re: How to get sufactant.gro, sufactant.top, (Mark Abraham)

[Mark Abraham]

ease? I've now had a slew of
>bounces from them.
>
>Thanks,
>
>Mark
>
>
>--
>
>Message: 3
>Date: Mon, 3 Jan 2011 17:20:23 -0800
>From: Ramachandran G
>Subject: [gmx-users] g_mindist
>To: gmx-users@gromacs.org
>Message-ID:
>
>Content-Type: text/plain; charset="iso-8859-1"
>
>Hi Gromacs users,
> I used g_mindist to calculate the minimum distance between a residue and
>a group of water molecules.
>Since distance is a length between two points in space, for the program
>considers the bunch of water molecules(15 number)
>what specific point does the group consider ? Thank you.
>
>Yours sincerely,
>Rama
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>Message: 4
>Date: Mon, 03 Jan 2011 20:29:02 -0500
>From: "Justin A. Lemkul"
>Subject: Re: [gmx-users] g_mindist
>To: Discussion list for GROMACS users
>Message-ID:<4d2277de.6080...@vt.edu>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
>Ramachandran G wrote:
>>  Hi Gromacs users,
>>  I used g_mindist to calculate the minimum distance between a residue
>>  and a group of water molecules.
>>  Since distance is a length between two points in space, for the program
>>  considers the bunch of water molecules(15 number)
>>  what specific point does the group consider ? Thank you.
>>
>
>The distance measured is that between the two closest atoms, whichever those 
may
>be.  Read the first few sentences of g_mindist -h.
>
>-Justin
>
>>  Yours sincerely,
>>  Rama
>>
>>
>>
>
>-- 
>

>
>Justin A. Lemkul
>Ph.D. Candidate
>ICTAS Doctoral Scholar
>MILES-IGERT Trainee
>Department of Biochemistry
>Virginia Tech
>Blacksburg, VA
>jalemkul[at]vt.edu | (540) 231-9080
>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>
>
>
>--
>
>Message: 5
>Date: Tue, 4 Jan 2011 11:59:53 +0530
>From: sreelakshmi ramesh
>Subject: Re: [gmx-users] The sum of the O-H distancesof the backbone
>hydrogenbonds ROH
>To: Discussion list for GROMACS users
>Message-ID:
>
>Content-Type: text/plain; charset="iso-8859-1"
>
>Thanks a lot for your reply..
>
>On Mon, Jan 3, 2011 at 6:07 PM, Mark Abrahamwrote:
>
>>  On 2/01/2011 2:18 PM, sreelakshmi ramesh wrote:
>>
>>>  Dear all,
>>>  I have a protein in water and i have simulated it for few
>>>  nanoseconds and i now i wanted to monitor the  The sum of the O-H distances
>>>  (in Å) of the backbone
>>>  hydrogen bonds ROH:i dono how to extract the value from the trajectory
>>>  file.Any siuggestion please.Thanks in advance
>>>
>>
>>  Look in section 7.4 of the manual for a suitable tool for extracting the
>>  raw distances. You'll need some other non-GROMACS tool to add them up.
>>
>>  Mark
>>  --
>>  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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>>
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>Message: 6
>Date: Tue, 4 Jan 2011 15:45:57 +0800 (CST)
>From: gromacs
>Subject: [gmx-users] How to get sufactant.gro, sufactant.top,
>To: gmx-users@gromacs.org
>Message-ID:<7bda4963.110c4.12d4ffd516f.coremail.ptf1...@163.com>
>Content-Type: text/plain; charset="gbk"
>
>Hi expert,
>
>I'd like to add sufactant to water. That means i should first get the 
sufactant.gro, and sufactant.top.
>
>Someone said that we cannot get sufactant.gro and sufactant.top through grompp 
()  sufactant.pdb. Because grompp  .pdb could mainly use for macro-biology big 
moleculars, which means some proteins etc.
>So that means we could not get correct  .gro, .top small molecules such as 
inorganic or small organic molecules (such asethanol).
>
>So how can we get the sufactant.gro, sufactant.top? and whic

[gmx-users] Re:Re: How to get sufactant.gro, sufactant.top, (Mark Abraham)

[gromacs]

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>
>Message: 4
>Date: Mon, 03 Jan 2011 20:29:02 -0500
>From: "Justin A. Lemkul" 
>Subject: Re: [gmx-users] g_mindist
>To: Discussion list for GROMACS users 
>Message-ID: <4d2277de.6080...@vt.edu>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
>Ramachandran G wrote:
>> Hi Gromacs users,
>> I used g_mindist to calculate the minimum distance between a residue 
>> and a group of water molecules.
>> Since distance is a length between two points in space, for the program 
>> considers the bunch of water molecules(15 number)
>> what specific point does the group consider ? Thank you.
>> 
>
>The distance measured is that between the two closest atoms, whichever those 
>may 
>be.  Read the first few sentences of g_mindist -h.
>
>-Justin
>
>> Yours sincerely,
>> Rama
>> 
>> 
>> 
>
>-- 
>
>
>Justin A. Lemkul
>Ph.D. Candidate
>ICTAS Doctoral Scholar
>MILES-IGERT Trainee
>Department of Biochemistry
>Virginia Tech
>Blacksburg, VA
>jalemkul[at]vt.edu | (540) 231-9080
>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>
>
>
>--
>
>Message: 5
>Date: Tue, 4 Jan 2011 11:59:53 +0530
>From: sreelakshmi ramesh 
>Subject: Re: [gmx-users] The sum of the O-H distancesof the backbone
>   hydrogenbonds ROH
>To: Discussion list for GROMACS users 
>Message-ID:
>   
>Content-Type: text/plain; charset="iso-8859-1"
>
>Thanks a lot for your reply..
>
>On Mon, Jan 3, 2011 at 6:07 PM, Mark Abraham wrote:
>
>> On 2/01/2011 2:18 PM, sreelakshmi ramesh wrote:
>>
>>> Dear all,
>>> I have a protein in water and i have simulated it for few
>>> nanoseconds and i now i wanted to monitor the  The sum of the O-H distances
>>> (in Å) of the backbone
>>> hydrogen bonds ROH:i dono how to extract the value from the trajectory
>>> file.Any siuggestion please.Thanks in advance
>>>
>>
>> Look in section 7.4 of the manual for a suitable tool for extracting the
>> raw distances. You'll need some other non-GROMACS tool to add them up.
>>
>> Mark
>> --
>> 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!
>> Please don't post (un)subscribe requests to the list. Use the www interface
>> or send it to gmx-users-requ...@gromacs.org.
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>>
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>Message: 6
>Date: Tue, 4 Jan 2011 15:45:57 +0800 (CST)
>From: gromacs 
>Subject: [gmx-users] How to get sufactant.gro, sufactant.top,
>To: gmx-users@gromacs.org
>Message-ID: <7bda4963.110c4.12d4ffd516f.coremail.ptf1...@163.com>
>Content-Type: text/plain; charset="gbk"
>
>Hi expert,
> 
>I'd like to add sufactant to water. That means i should first get the 
>sufactant.gro, and sufactant.top.
> 
>Someone said that we cannot get sufactant.gro and sufactant.top through grompp 
>()  sufactant.pdb. Because grompp  .pdb could mainly use for macro-biology big 
>moleculars, which means some proteins etc.
>So that means we could not get correct  .gro, .top small molecules such as 
>inorganic or small organic molecules (such asethanol).
> 
>So how can we get the sufactant.gro, sufactant.top? and which force field 
>should we choose for ordinary simulation? I know we often use ffoplass force 
>field for solution.
> 
>Tiefeng
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>--
>
>Message: 7
>Date: Tue, 04 Jan 2011 19:18:10 +1100
>From: Mark Abraham 
>Subject: Re: [gmx-users] How to get sufactant.gro, sufactant.top,
>To: Discussion list for GROMACS users 
>Message-ID: <7690a1161265.4d237...@anu.edu.au>
>Content-Type: text/plain; charset="iso-8859-1"
>
>On 01/04/11, gromacs   wrote:

Re: [gmx-users] query for protein-igand binding energy calculation using LIE and Gromacs simulation

[Mark Abraham]

On 5/01/2011 5:06 PM, devawati dutta wrote:

Dear Sir,
  I am using Gromacs 3.3.2 version for molecular dynamics 
simulation of my protein-ligand complex. I want to calculate the free 
energy of binding through LIE method. While extracting the LJ and 
coulombic energy values using g_energy command,there are many options 
like LJ-14, LJ-SR, LJ-LR, Coul-14, Coul-SR, Coul-recip etc. I am 
unable to decide which values should I use for free energy 
calculation .Which of the following options should I consider.

1. Should I use only LJ-SR and coul-SR?
2. Should I use the total energy values i.e LJ-SR+LJ-LR?


LIE does not work with PME. This issue has been discussed on this list 
many times, if you search the list archives.


Also, unless you need continuity with earlier work, you should upgrade 
to the latest GROMACS for much better performance and fewer bugs.


Mark
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[gmx-users] query for protein-igand binding energy calculation using LIE and Gromacs simulation

[devawati dutta]

Dear Sir,
  I am using Gromacs 3.3.2 version for molecular dynamics
simulation of my protein-ligand complex. I want to calculate the free energy
of binding through LIE method. While extracting the LJ and coulombic energy
values using g_energy command,there are many options like LJ-14, LJ-SR,
LJ-LR, Coul-14, Coul-SR, Coul-recip etc. I am unable to decide which values
should I use for free energy calculation .Which of the following options
should I consider.
1. Should I use only LJ-SR and coul-SR?
2. Should I use the total energy values i.e LJ-SR+LJ-LR?

Your's sincerely
Devawati Dutta
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Re: [gmx-users] g_sdf

[Justin A. Lemkul]

Nilesh Dhumal wrote:

Hello,
I am trying to calculate g_sdf for my system (ionic liquids + water).

I interested in distribution of anions and waters around cations.

I used following command
g_sdf -f 3.trr -n emi-etso4-64-no.ndx -s 3.tpr  -o -r -mode 2

I found all the corrdinates in refmol.gro are zero.

I calculated distribution of anions around cations

g_sdf -f 3.trr -n emi-etso4-64-no.ndx -s 3.tpr  -o -r

I got proper corrdinates in refmol.gro.

Why I am getting corrdinates zero for mode 2.



You're not using the command properly.  Read g_sdf -h.

You may find g_spatial more useful; in fact, g_sdf has been removed from version 
4.5 while g_spatial was maintained.  g_sdf is better suited for water and not 
much else.


-Justin


Nilesh






--


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


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[gmx-users] g_sdf

[Nilesh Dhumal]

Hello,
I am trying to calculate g_sdf for my system (ionic liquids + water).

I interested in distribution of anions and waters around cations.

I used following command
g_sdf -f 3.trr -n emi-etso4-64-no.ndx -s 3.tpr  -o -r -mode 2

I found all the corrdinates in refmol.gro are zero.

I calculated distribution of anions around cations

g_sdf -f 3.trr -n emi-etso4-64-no.ndx -s 3.tpr  -o -r

I got proper corrdinates in refmol.gro.

Why I am getting corrdinates zero for mode 2.

Nilesh




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Re: [gmx-users] CNT

[Mark Abraham]

On 01/05/11, mustafa bilsel   wrote:
> Hi all,
> Could you tell me a program to obtain topol.top for a CNT?
> In CNT.pdb residues are efined as UNK.
> 
There may be some useful content here 
http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube

Mark
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Re: [gmx-users] CNT

[Justin A. Lemkul]

mustafa bilsel wrote:

Hi all,
Could you tell me a program to obtain topol.top for a CNT?
In CNT.pdb residues are efined as UNK.


g_x2top is probably your best bet.  Please have a thorough look through both the 
Gromacs site and the mailing list archive.  Issues related to CNTs (especially 
their topologies) have been posted countless times.


-Justin



best wishes
mustafa



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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] CNT

[wibke . sudholt]

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[gmx-users] CNT

[mustafa bilsel]

Hi all,
Could you tell me a program to obtain topol.top for a CNT?
In CNT.pdb residues are efined as UNK.

best wishes
mustafa
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Re: [gmx-users] Constraints and efficency

[Mark Abraham]

On 5/01/2011 5:53 AM, Elton Carvalho wrote:

Hello, fellow GROMACS users!

I noticed many users applying constraints to their simulations, be it
SETTLE to water molecules or LINCS to some other species. This brings
about an efficiency concern once that after each Verlet step some
systems of coupled equations must be solved in order to apply these
constraints.

My question is: water molecules are the most numerous species in a
solvated simulation, and the SETTLE algorithm seems to take O(n) time
for each molecule (Hence, O(3) per molecule), thus yelding O(M) to
apply SETTLE to all M water molecules in a system, per MD step. Why is
this beneficial? Does the larger timestep allowed by eliminating
high-frequency O-H vibrations outweigh the time needed by SETTLE?


Most definitely. Typical GROMACS simulations report up to a few percent 
of the total simulation time is spent in dealing with constraints. If 
the use of constraints permitted a 2fs timestep rather than 0.5fs, then 
it's nearly a four-fold speed-up.



Any other reason I failed to notice?


I seem to recall that bond constraints are held to model the essential 
QM nature of interatomic bonds better than a Morse or harmonic potential 
(particularly for bonds to hydrogen). I don't recall a reference for 
that offhand, unfortunately. Perhaps the original SHAKE paper.



Same thing for LINCS in, say, surfactant molecules: Is there any other
reason to do this other than shave off higher frequencies (C-H for
instance) and allow a larger timestep?

The only reason I see to constrain movement other than that fraquency
shaving (and, of course, isolating some behaviour of interest, but
this is case-specific) would be to reduce the number of dimensions of
the phase space and save computatuon time, but, as implemented, this
doesn't seem possible with the code as is.


Various coarse-graining approaches exist to take advantage of that kind 
of saving, but they also gain from the higher maximum time step.


Mark


My molecular dynamics background is based on Cerius2, so please pardon
some lack of intimacy with GROMACS behaviour.

Regards,


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Re: [gmx-users] percentage of secondary structure

[Mark Abraham]

On 5/01/2011 12:35 AM, ahmet yıldırım wrote:
I get the residue versus time ( secondary structure graph) using 
do_dssp tool. I want to get the percentage value(alpha helix, beta 
sheet, coil ...) of secondary structure. 


Please say this in the *first* email. Giving a full description of what 
you have done and what you got as output and why it isn't yet suitable 
runs a much lower risk of wasting the time of everyone who reads your 
email and has to guess what help you want. See 
http://www.gromacs.org/Support - had you followed these steps you'd have 
probably had an answer from Justin in one email.


Mark


For example:

Secondary structure percentage (%):
Helix:51.6
B-sheet:0
Random coil:24.0
Turn:24.4

04 Ocak 2011 14:59 tarihinde Mark Abraham > yazdı:


On 4/01/2011 11:38 PM, ahmet yıldırım wrote:

Dear Mark,

I will do by using the g_analyze tool but I do not know how to
use it.


There's a section in Appendix D of the manual for each tool, or
you can use the -h argument to the tool to get the same information.

Either way, you haven't got the right tool. Hint: it's a "protein
specific analysis"

Mark




Thanks

2011/1/4 Mark Abraham mailto:mark.abra...@anu.edu.au>>

On 4/01/2011 8:33 PM, ahmet yıldırım wrote:

Hi,

How can I calculate the percentages (alpha helix, beta
sheet, coil ...) of secondary structure?


Look in manual section 7.4 for a suitable tool.

Mark
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-- 
Ahmet YILDIRIM



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--
Ahmet YILDIRIM


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Re: [gmx-users] Simulations on GPU

[Rossen Apostolov]

On 1/4/11 3:16 PM, Francesco Oteri wrote:

Maybe the used force-field is wrong.
mdrun-gpu is able to use the AMBER forcefield, but it is not possible 
using gromos force-field.

When gromos force-field is used, the output is full of NaN

Is that the case?

mdrun should complain and exit if the FF isn't supported.

Rossen
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[gmx-users] g_sdf

[Nilesh Dhumal]

Hello,
I am trying to calculate g_sdf for my system (ionic liquids + water).

I interested in distribution of anions and waters around cations.

I used following command
g_sdf -f 3.trr -n emi-etso4-64-no.ndx -s 3.tpr  -o -r -mode 2

I found all the corrdinates in refmol.gro are zero.

I calculated distribution of anions around cations

g_sdf -f 3.trr -n emi-etso4-64-no.ndx -s 3.tpr  -o -r

I got proper corrdinates in refmol.gro.

Why I am getting corrdinates zero for mode 2.

Nilesh



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[gmx-users] Constraints and efficency

[Elton Carvalho]

Hello, fellow GROMACS users!

I noticed many users applying constraints to their simulations, be it
SETTLE to water molecules or LINCS to some other species. This brings
about an efficiency concern once that after each Verlet step some
systems of coupled equations must be solved in order to apply these
constraints.

My question is: water molecules are the most numerous species in a
solvated simulation, and the SETTLE algorithm seems to take O(n) time
for each molecule (Hence, O(3) per molecule), thus yelding O(M) to
apply SETTLE to all M water molecules in a system, per MD step. Why is
this beneficial? Does the larger timestep allowed by eliminating
high-frequency O-H vibrations outweigh the time needed by SETTLE? Any
other reason I failed to notice?

Same thing for LINCS in, say, surfactant molecules: Is there any other
reason to do this other than shave off higher frequencies (C-H for
instance) and allow a larger timestep?

The only reason I see to constrain movement other than that fraquency
shaving (and, of course, isolating some behaviour of interest, but
this is case-specific) would be to reduce the number of dimensions of
the phase space and save computatuon time, but, as implemented, this
doesn't seem possible with the code as is.

My molecular dynamics background is based on Cerius2, so please pardon
some lack of intimacy with GROMACS behaviour.

Regards,
-- 
Elton Carvalho
Tel.: +55 11 3091-6985/6922
Dept Física dos Materiais e Mecânica
Instituto de Física
Universidade de São Paulo
P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil
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Re: [gmx-users] percentage of secondary structure

[ahmet yıldırım]

Dear Justin,

I understand. Thank you very much.

04 Ocak 2011 20:36 tarihinde Justin A. Lemkul  yazdı:

>
>
> ahmet yıldırım wrote:
>
>> Dear Justin,
>>
>> Thanks for your reply. There are not percentage of secondary structure in
>> "scount.xvg".
>>
>
> I know that.  But this is all the information you need.  If you have a
> count of how many residues are in a particular conformation over time, all
> you have to do is divide by the number of total residues and you have your
> percentage.
>
> Gromacs isn't going to do everything for you, but it quite often has the
> capability to give you whatever raw data you need to properly manipulate.
>
> -Justin
>
>  The content of the "scount.xvg" file are as the following:
>>
>> # This file was created Tue Jan  4 19:28:47 2011
>> # by the following command:
>> # do_dssp -s run.tpr -f run.xtc
>> #
>> # do_dssp is part of G R O M A C S:
>> #
>> # GROup of MAchos and Cynical Suckers
>> #
>> @title "Secondary Structure"
>> @xaxis  label "Time (ps)"
>> @yaxis  label "Number of Residues"
>> @TYPE xy
>> @ subtitle "Structure = A-Helix + B-Sheet + B-Bridge + Turn"
>> @ view 0.15, 0.15, 0.75, 0.85
>> @ legend on
>> @ legend box on
>> @ legend loctype view
>> @ legend 0.78, 0.8
>> @ legend length 2
>> @ s0 legend "Structure"
>> @ s1 legend "Coil"
>> @ s2 legend "B-Sheet"
>> @ s3 legend "B-Bridge"
>> @ s4 legend "Bend"
>> @ s5 legend "Turn"
>> @ s6 legend "A-Helix"
>> @ s7 legend "3-Helix"
>>   0   1281914 11711   102 0
>> 0.2   1311914 11414   102 0
>> 0.4   1321914 1132394 0
>> 0.6   1301914 11512   103 0
>> 0.8   1321914 1131998 0
>>   1   1302114 1132887 0
>> .
>>
>> 04 Ocak 2011 20:04 tarihinde Justin A. Lemkul > jalem...@vt.edu>> yazdı:
>>
>>
>>
>>
>>ahmet yıldırım wrote:
>>
>>Dear Justin,
>>
>>I am using the commands as the following.
>>do_dssp -s run.tpr -f run.xtc
>>xpm2ps -f ss.xpm -o ss.eps
>>
>>You said "Have a look at the other output file do_dssp gives
>>you". which one should I look?
>>
>>
>>Well, there's another output file from do_dssp called "scount.xvg,"
>>which should  be almost exactly what you need.  See do_dssp -h for a
>>description, then look at the file yourself.
>>
>>-Justin
>>
>>Thanks
>>
>>04 Ocak 2011 15:51 tarihinde Justin A. Lemkul > >
>>>> yazdı:
>>
>>
>>
>>
>>   ahmet yıldırım wrote:
>>
>>   I get the residue versus time ( secondary structure
>>graph) using
>>   do_dssp tool. I want to get the percentage value(alpha
>> helix,
>>   beta sheet, coil ...) of secondary structure. For example:
>>
>>   Secondary structure percentage (%):
>>   Helix:51.6
>>   B-sheet:0
>>   Random coil:24.0
>>   Turn:24.4
>>
>>
>>   Have a look at the other output file do_dssp gives you.
>>
>>   -Justin
>>
>>
>>   04 Ocak 2011 14:59 tarihinde Mark Abraham
>>   mailto:mark.abra...@anu.edu.au>
>>>
>>   >
>>   >>
>>
>>  On 4/01/2011 11:38 PM, ahmet yıldırım wrote:
>>
>>  Dear Mark,
>>
>>  I will do by using the g_analyze tool but I do not
>>know
>>   how to use it.
>>
>>
>>  There's a section in Appendix D of the manual for each
>>tool,
>>   or you
>>  can use the -h argument to the tool to get the same
>>information.
>>
>>  Either way, you haven't got the right tool. Hint: it's
>>a "protein
>>  specific analysis"
>>
>>  Mark
>>
>>
>>
>>  Thanks
>>
>>  2011/1/4 Mark Abraham >
>>   >>
>>  >
>>   >>
>>
>>  On 4/01/2011 8:33 PM, ahmet yıldırım wrote:
>>
>>  Hi,
>>
>>  How can I calculate the percentages (alpha
>>helix,
>>   beta
>>  sheet, coil ...) of secondary structure?
>>
>>
>>  

Re: [gmx-users] percentage of secondary structure

[Justin A. Lemkul]

ahmet yıldırım wrote:

Dear Justin,

Thanks for your reply. There are not percentage of secondary structure 
in "scount.xvg".


I know that.  But this is all the information you need.  If you have a count of 
how many residues are in a particular conformation over time, all you have to do 
is divide by the number of total residues and you have your percentage.


Gromacs isn't going to do everything for you, but it quite often has the 
capability to give you whatever raw data you need to properly manipulate.


-Justin


The content of the "scount.xvg" file are as the following:

# This file was created Tue Jan  4 19:28:47 2011
# by the following command:
# do_dssp -s run.tpr -f run.xtc
#
# do_dssp is part of G R O M A C S:
#
# GROup of MAchos and Cynical Suckers
#
@title "Secondary Structure"
@xaxis  label "Time (ps)"
@yaxis  label "Number of Residues"
@TYPE xy
@ subtitle "Structure = A-Helix + B-Sheet + B-Bridge + Turn"
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "Structure"
@ s1 legend "Coil"
@ s2 legend "B-Sheet"
@ s3 legend "B-Bridge"
@ s4 legend "Bend"
@ s5 legend "Turn"
@ s6 legend "A-Helix"
@ s7 legend "3-Helix"
   0   1281914 11711   102 0
 0.2   1311914 11414   102 0
 0.4   1321914 1132394 0
 0.6   1301914 11512   103 0
 0.8   1321914 1131998 0
   1   1302114 1132887 0
.

04 Ocak 2011 20:04 tarihinde Justin A. Lemkul > yazdı:




ahmet yıldırım wrote:

Dear Justin,

I am using the commands as the following.
do_dssp -s run.tpr -f run.xtc
xpm2ps -f ss.xpm -o ss.eps

You said "Have a look at the other output file do_dssp gives
you". which one should I look?


Well, there's another output file from do_dssp called "scount.xvg,"
which should  be almost exactly what you need.  See do_dssp -h for a
description, then look at the file yourself.

-Justin

Thanks

04 Ocak 2011 15:51 tarihinde Justin A. Lemkul mailto:jalem...@vt.edu> >> yazdı:




   ahmet yıldırım wrote:

   I get the residue versus time ( secondary structure
graph) using
   do_dssp tool. I want to get the percentage value(alpha helix,
   beta sheet, coil ...) of secondary structure. For example:

   Secondary structure percentage (%):
   Helix:51.6
   B-sheet:0
   Random coil:24.0
   Turn:24.4


   Have a look at the other output file do_dssp gives you.

   -Justin


   04 Ocak 2011 14:59 tarihinde Mark Abraham
   mailto:mark.abra...@anu.edu.au>
>
   
   
   >
  
   

>
  
   

Re: [gmx-users] percentage of secondary structure

[ahmet yıldırım]

Dear Justin,

Thanks for your reply. There are not percentage of secondary structure in
"scount.xvg".
The content of the "scount.xvg" file are as the following:

# This file was created Tue Jan  4 19:28:47 2011
# by the following command:
# do_dssp -s run.tpr -f run.xtc
#
# do_dssp is part of G R O M A C S:
#
# GROup of MAchos and Cynical Suckers
#
@title "Secondary Structure"
@xaxis  label "Time (ps)"
@yaxis  label "Number of Residues"
@TYPE xy
@ subtitle "Structure = A-Helix + B-Sheet + B-Bridge + Turn"
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "Structure"
@ s1 legend "Coil"
@ s2 legend "B-Sheet"
@ s3 legend "B-Bridge"
@ s4 legend "Bend"
@ s5 legend "Turn"
@ s6 legend "A-Helix"
@ s7 legend "3-Helix"
   0   1281914 11711   102 0
 0.2   1311914 11414   102 0
 0.4   1321914 1132394 0
 0.6   1301914 11512   103 0
 0.8   1321914 1131998 0
   1   1302114 1132887 0
.

04 Ocak 2011 20:04 tarihinde Justin A. Lemkul  yazdı:

>
>
> ahmet yıldırım wrote:
>
>> Dear Justin,
>>
>> I am using the commands as the following.
>> do_dssp -s run.tpr -f run.xtc
>> xpm2ps -f ss.xpm -o ss.eps
>>
>> You said "Have a look at the other output file do_dssp gives you". which
>> one should I look?
>>
>>
> Well, there's another output file from do_dssp called "scount.xvg," which
> should  be almost exactly what you need.  See do_dssp -h for a description,
> then look at the file yourself.
>
> -Justin
>
>  Thanks
>>
>> 04 Ocak 2011 15:51 tarihinde Justin A. Lemkul > jalem...@vt.edu>> yazdı:
>>
>>
>>
>>
>>ahmet yıldırım wrote:
>>
>>I get the residue versus time ( secondary structure graph) using
>>do_dssp tool. I want to get the percentage value(alpha helix,
>>beta sheet, coil ...) of secondary structure. For example:
>>
>>Secondary structure percentage (%):
>>Helix:51.6
>>B-sheet:0
>>Random coil:24.0
>>Turn:24.4
>>
>>
>>Have a look at the other output file do_dssp gives you.
>>
>>-Justin
>>
>>
>>04 Ocak 2011 14:59 tarihinde Mark Abraham
>>mailto:mark.abra...@anu.edu.au>
>>>>> yazdı:
>>
>>
>>   On 4/01/2011 11:38 PM, ahmet yıldırım wrote:
>>
>>   Dear Mark,
>>
>>   I will do by using the g_analyze tool but I do not know
>>how to use it.
>>
>>
>>   There's a section in Appendix D of the manual for each tool,
>>or you
>>   can use the -h argument to the tool to get the same information.
>>
>>   Either way, you haven't got the right tool. Hint: it's a
>> "protein
>>   specific analysis"
>>
>>   Mark
>>
>>
>>
>>   Thanks
>>
>>   2011/1/4 Mark Abraham >
>>   >>>
>>
>>
>>   On 4/01/2011 8:33 PM, ahmet yıldırım wrote:
>>
>>   Hi,
>>
>>   How can I calculate the percentages (alpha helix,
>>beta
>>   sheet, coil ...) of secondary structure?
>>
>>
>>   Look in manual section 7.4 for a suitable tool.
>>
>>   Mark
>>   -- gmx-users mailing list
>> gmx-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!
>>   Please don't post (un)subscribe requests to the list.
>>Use the
>>   www interface or send it to
>>gmx-users-requ...@gromacs.org
>>
>>   >>.
>>
>>   Can't post? Read
>>http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
>>
>>   -- Ahmet YILDIRIM
>>
>>
>>
>>   --
>>   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!
>>   Please d

Re: [gmx-users] percentage of secondary structure

[Justin A. Lemkul]

ahmet yıldırım wrote:

Dear Justin,

I am using the commands as the following.
do_dssp -s run.tpr -f run.xtc
xpm2ps -f ss.xpm -o ss.eps

You said "Have a look at the other output file do_dssp gives you". which 
one should I look?




Well, there's another output file from do_dssp called "scount.xvg," which should 
 be almost exactly what you need.  See do_dssp -h for a description, then look 
at the file yourself.


-Justin


Thanks

04 Ocak 2011 15:51 tarihinde Justin A. Lemkul > yazdı:




ahmet yıldırım wrote:

I get the residue versus time ( secondary structure graph) using
do_dssp tool. I want to get the percentage value(alpha helix,
beta sheet, coil ...) of secondary structure. For example:

Secondary structure percentage (%):
Helix:51.6
B-sheet:0
Random coil:24.0
Turn:24.4


Have a look at the other output file do_dssp gives you.

-Justin


04 Ocak 2011 14:59 tarihinde Mark Abraham
mailto:mark.abra...@anu.edu.au>
>> yazdı:


   On 4/01/2011 11:38 PM, ahmet yıldırım wrote:

   Dear Mark,

   I will do by using the g_analyze tool but I do not know
how to use it.


   There's a section in Appendix D of the manual for each tool,
or you
   can use the -h argument to the tool to get the same information.

   Either way, you haven't got the right tool. Hint: it's a "protein
   specific analysis"

   Mark



   Thanks

   2011/1/4 Mark Abraham mailto:mark.abra...@anu.edu.au>
   >>


   On 4/01/2011 8:33 PM, ahmet yıldırım wrote:

   Hi,

   How can I calculate the percentages (alpha helix,
beta
   sheet, coil ...) of secondary structure?


   Look in manual section 7.4 for a suitable tool.

   Mark
   -- gmx-users mailing list  
 gmx-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!
   Please don't post (un)subscribe requests to the list.
Use the
   www interface or send it to
gmx-users-requ...@gromacs.org

   >.

   Can't post? Read
http://www.gromacs.org/Support/Mailing_Lists




   -- Ahmet YILDIRIM



   --
   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!
   Please don't post (un)subscribe requests to the list. Use the
   www interface or send it to gmx-users-requ...@gromacs.org

   >.

   Can't post? Read http://www.gromacs.org/Support/Mailing_Lists




-- 
Ahmet YILDIRIM



-- 



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



-- 
gmx-users mailing listgmx-users@gromacs.org


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Please search the archive at
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.
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--
Ahmet YILDIRIM


--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem

Re: [gmx-users] percentage of secondary structure

[ahmet yıldırım]

Dear Justin,

I am using the commands as the following.
do_dssp -s run.tpr -f run.xtc
xpm2ps -f ss.xpm -o ss.eps

You said "Have a look at the other output file do_dssp gives you".
which one should
I look?

Thanks

04 Ocak 2011 15:51 tarihinde Justin A. Lemkul  yazdı:

>
>
> ahmet yıldırım wrote:
>
>> I get the residue versus time ( secondary structure graph) using do_dssp
>> tool. I want to get the percentage value(alpha helix, beta sheet, coil ...)
>> of secondary structure. For example:
>>
>> Secondary structure percentage (%):
>> Helix:51.6
>> B-sheet:0
>> Random coil:24.0
>> Turn:24.4
>>
>
> Have a look at the other output file do_dssp gives you.
>
> -Justin
>
>
>> 04 Ocak 2011 14:59 tarihinde Mark Abraham > mark.abra...@anu.edu.au>> yazdı:
>>
>>
>>On 4/01/2011 11:38 PM, ahmet yıldırım wrote:
>>
>>>Dear Mark,
>>>
>>>I will do by using the g_analyze tool but I do not know how to use it.
>>>
>>
>>There's a section in Appendix D of the manual for each tool, or you
>>can use the -h argument to the tool to get the same information.
>>
>>Either way, you haven't got the right tool. Hint: it's a "protein
>>specific analysis"
>>
>>Mark
>>
>>
>>
>>>Thanks
>>>
>>>2011/1/4 Mark Abraham >>>
>>>
>>>
>>>On 4/01/2011 8:33 PM, ahmet yıldırım wrote:
>>>
>>>Hi,
>>>
>>>How can I calculate the percentages (alpha helix, beta
>>>sheet, coil ...) of secondary structure?
>>>
>>>
>>>Look in manual section 7.4 for a suitable tool.
>>>
>>>Mark
>>>-- 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!
>>>Please don't post (un)subscribe requests to the list. Use the
>>>www interface or send it to gmx-users-requ...@gromacs.org
>>>.
>>>
>>>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>>
>>>
>>>
>>>-- Ahmet YILDIRIM
>>>
>>
>>
>>--
>>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!
>>Please don't post (un)subscribe requests to the list. Use the
>>www interface or send it to gmx-users-requ...@gromacs.org
>>.
>>
>>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
>>
>> --
>> Ahmet YILDIRIM
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
>
> --
> 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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> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Ahmet YILDIRIM
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
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Re: [gmx-users] help regarding simulation

[Justin A. Lemkul]

onetwo wrote:

Hello All,

I want to know one thing that if MD could be used in my case, i have a 
protein for which crystal structure is known with a conenzyme bound to 
it. It is given in literature that related proteins of this family shows 
large conformational change near the substrate binding region when the 
substrate binds to the protein.
In absence of the crystal structure, if doing simulation with the 
protein complexed with the coenzyme and the docked substrate will be 
useful? , i.e, if this complex with the help of the simulation could be 
capable of displaying such conformational change ? or what could be the 
probable limitaions ?




Possibly.  The limitation is time.  Conformational changes are generally slow, 
so your simulations would likely have to be fairly long.


-Justin


Regards and thanks for your time.





--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] Re: Average box size

[Tsjerk Wassenaar]

Navjeet,

The average lengths you already mentioned in your first mail:

>>> Box-X  Box-Y  Box-Z Volume   Density (SI)
>>>   4.44479e+004.49781e+004.88259e+009.76118e+011.04364e+03

You also mentioned you used isotropic PC:

>>> I did NPT simulation for 30 ns using triclinic box (-angles 88.30,
>>> 107.40, 112.20) and Isotropic pressure coupling.

Then the box only gets scaled during the simulation, with no changes
of one vector relative to the other. Then to set the box of your end
structure to match the average volume also means scaling. That means
taking the ratio of the average X-length and the actual X-length, and
feed that as a scaling factor...
Then again, you don't actually need to calculate anything, just think
a little bit harder. You're average box comes with an average density.
editconf has an option to scale the box to get a specific density, so
you can fetch the average density, given above and do:

editconf -f end.gro -o average.gro -density 1.04364e+03

Then go on with your NVT run using average.gro as input (don't forget
the energy minimization!).

Hope it helps,

Tsjerk

On Tue, Jan 4, 2011 at 3:03 PM, Navjeet Ahalawat  wrote:
> Hi Tsjerk,
>
> Thanks for your clarifications. I still couldn't follow how I can calculate
> the scaling factor. As I wrote earlier, I ran NPT simulation for 
> equilibration.
>
> Now to start the NVT production run, I need to know the AVERAGE LENGTHS
> (a, b, c) of the triclinic box vectors so that I can generate the
> triclinic box with the
> help of the corresponding angles (88.30, 107.40, 112.20) using the
> command "editconf".
>
> Now I understand that the box-x, box-y, and box-z represents the diagonal
> elements of triangular matrix and the average volume of my triclinic box
> is the product of these diagonal elements. However, as I understand the
> command "editconf" requires the length of the box vectors and the three angles
> to create a triclinic box.
>
> I would greatly appreciate if you could please let me know the command(s) that
> I would require to use to achieve my goal.
>
>
>
>
> Message: 4
> Date: Tue, 4 Jan 2011 12:35:36 +0100
> From: Tsjerk Wassenaar 
> Subject: Re: [gmx-users] Re: Average box size
> To: Discussion list for GROMACS users 
> Message-ID:
>        
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Navjeet,
>
> These you had in the log file as you showed in your mail. Note that
> you use isotropic pressure coupling, so you just need to calculate a
> scaling factor, which you can give to editconf to change your system
> to match the average box size.
>
>  Cheers,
>
> Tsjerk
>
> On Tue, Jan 4, 2011 at 12:03 PM, Navjeet Ahalawat  
> wrote:
>> Hi Tsjerk,
>>
>> Thanks for reply, Please can you tell me how can I get the average box
>> length (a b c) of my triclinic box for my next step.
>>
>>> Message: 2
>>> Date: Mon, 3 Jan 2011 18:17:15 +0100
>>> From: Tsjerk Wassenaar 
>>> Subject: Re: [gmx-users] Average box size
>>> To: Discussion list for GROMACS users 
>>> Message-ID:
>>>        
>>> Content-Type: text/plain; charset="iso-8859-1"
>>>
>>> Hi Navjeet,
>>>
>>> The box is defined as a triangular matrix, so the volume equals the product
>>> of the diagonal elements.
>>>
>>> Hope it helps,
>>>
>>> Tsjerk
>>>
>>> On Jan 3, 2011 5:57 PM, "Navjeet Ahalawat"  wrote:
>>>
>>> Hi all
>>>
>>> I did NPT simulation for 30 ns using triclinic box (-angles 88.30,
>>> 107.40, 112.20) and Isotropic pressure coupling. Now i want to use
>>> average box size for production run (NVT). But I am confused because i
>>> am not able to get the meaning of the output values of the log file.
>>>
>>>
>>> Log file output.
>>>
>>>       <==  ###  ==>
>>>       <  A V E R A G E S  >
>>>       <==  ###  ==>
>>>
>>>  Energies (kJ/mol)
>>>          Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>>>   9.31715e+02    2.35558e+03    1.63083e+02    5.15266e+03    1.79003e+03
>>>    Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
>>>   1.63211e+04    2.86765e+04   -1.72320e+05   -4.98704e+04   -1.66800e+05
>>>   Kinetic En.   Total Energy    Temperature Pressure (bar)  Cons. rmsd ()
>>>   1.27874e+04   -1.54012e+05    1.49958e+02    1.07033e+00    0.0e+00
>>>
>>>         Box-X          Box-Y          Box-Z         Volume   Density (SI)
>>>   4.44479e+00    4.49781e+00    4.88259e+00    9.76118e+01    1.04364e+03
>>>
>>> If Box-X Box-Y Box-Z represent average value of  a b c then volume
>>> does not correspond to my triclinic box because its just
>>> multiplication of Box-X Box-Y Box-Z. So Please can anybody help me
>>> which volume should I consider for next NVT production run.
>>>
>>> Any help in this regard would be highly appreciated.
>>>
>>>
>>> Thanks & Regards,
>>> Navjeet Ahalawat
>> --
>> gmx-users mailing list    gmx-us...@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at 
>> ht

[gmx-users] help regarding simulation

[onetwo]

Hello All,

I want to know one thing that if MD could be used in my case, i have a protein 
for which crystal structure is known  with a conenzyme bound to it. It is given 
in literature that related proteins of this family shows large conformational 
change near the substrate binding region when the substrate binds to the 
protein.
In absence of the crystal structure, if doing simulation with the protein 
complexed with the coenzyme and the docked substrate will be useful? , i.e, if 
this complex with the help of the simulation could be capable of displaying 
such conformational change ? or what could be the probable limitaions ?

Regards and thanks for your time.
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Re: [gmx-users] Simulations on GPU

[Francesco Oteri]

Maybe the used force-field is wrong.
mdrun-gpu is able to use the AMBER forcefield, but it is not possible 
using gromos force-field.

When gromos force-field is used, the output is full of NaN

Il 12/10/2010 03:00, Igor Leontyev ha scritto:
Now I am able to run simulations on GPU but the output is weird. For 
example, temperature drops down to 270K while ref_t=298 
(Tcoupl=andersen). Moreover, after several hours of simulations 
mdrun-gpu starts to output "NAN" energies and hangs up. Pre-run and 
post-run GPU memory test is always passed. The graphics card is that 
provided with HP desktops (might be MSI) NVIDIA GTX260 with 1.8Gb 
memory. The output of mdrun and mdrun-gpu versions of Gromacs is given 
bellow. Any ideas? Thanks.


Igor

 


Log file opened on Fri Oct  8 14:46:51 2010
Host: powerpc  pid: 32083  nodeid: 0  nnodes:  4
The Gromacs distribution was built Thu Sep 30 14:42:48 PDT 2010 by
leont...@powerpc (Linux 2.6.32-22-generic x86_64)


:-)  G  R  O  M  A  C  S  (-:

  Gromacs Runs One Microsecond At Cannonball Speeds

   :-)  VERSION 4.5.1  (-:

   Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
 Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
   Gerrit Groenhof, Peter Kasson, Per Larsson, Peiter Meulenhoff,
 Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schultz,
   Michael Shirts, Alfons Sijbers, Peter Tieleman,

  Berk Hess, David van der Spoel, and Erik Lindahl.

  Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   Copyright (c) 2001-2010, The GROMACS development team at
   Uppsala University & The Royal Institute of Technology, Sweden.
   check out http://www.gromacs.org for more information.

This program is free software; you can redistribute it and/or
 modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.

 :-)  /usr/local/opt/bin/gromacs/gromacs-4.5.1/bin/mdrun_mpich2  (-:



Input Parameters:
  integrator   = md
  nsteps   = 1
  init_step= 0
  ns_type  = Grid
  nstlist  = 10
  ndelta   = 2
  nstcomm  = 1003
  comm_mode= Linear
  nstlog   = 1000
  nstxout  = 5000
  nstvout  = 1000
  nstfout  = 0
  nstcalcenergy= 10
  nstenergy= 1000
  nstxtcout= 0
  init_t   = 0
  delta_t  = 0.001
  xtcprec  = 1000
  nkx  = 54
  nky  = 60
  nkz  = 90
  pme_order= 6
  ewald_rtol   = 1e-05
  ewald_geometry   = 0
  epsilon_surface  = 0
  optimize_fft = TRUE
  ePBC = xyz
  bPeriodicMols= FALSE
  bContinuation= FALSE
  bShakeSOR= FALSE
  etc  = Andersen
  nsttcouple   = 10
  epc  = Berendsen
  epctype  = Isotropic
  nstpcouple   = 10
  tau_p= 0.5
  ref_p (3x3):
 ref_p[0]={ 1.01325e+00,  0.0e+00,  0.0e+00}
 ref_p[1]={ 0.0e+00,  1.01325e+00,  0.0e+00}
 ref_p[2]={ 0.0e+00,  0.0e+00,  1.01325e+00}
  compress (3x3):
 compress[0]={ 4.5e-05,  0.0e+00,  0.0e+00}
 compress[1]={ 0.0e+00,  4.5e-05,  0.0e+00}
 compress[2]={ 0.0e+00,  0.0e+00,  4.5e-05}
  refcoord_scaling = No
  posres_com (3):
 posres_com[0]= 0.0e+00
 posres_com[1]= 0.0e+00
 posres_com[2]= 0.0e+00
  posres_comB (3):
 posres_comB[0]= 0.0e+00
 posres_comB[1]= 0.0e+00
 posres_comB[2]= 0.0e+00
  andersen_seed= 815131
  rlist= 1.2
  rlistlong= 1.2
  rtpi = 0.05
  coulombtype  = PME
  rcoulomb_switch  = 0
  rcoulomb = 1.2
  vdwtype  = Cut-off
  rvdw_switch  = 0
  rvdw = 1.2
  epsilon_r= 1
  epsilon_rf   = 1
  tabext   = 1
  implicit_solvent = No
  gb_algorithm = Still
  gb_epsilon_solvent   = 80
  nstgbradii   = 1
  rgbradii = 1
  gb_saltconc  = 0
  gb_obc_alpha = 1
  gb_obc_beta  = 0.8
  gb_obc_gamma = 4.85
  gb_dielectric_offset = 0.009
  sa_algorithm = No
  sa_surface_tension   = 2.092
  DispCorr = EnerPres
  free_energy  = no
  init_lambda  = 0
  delta_lambda = 0
  n_foreign_lambda = 0
  sc_alpha = 0
  sc_power = 0
  sc_sigma = 0.3
  sc_sigma_min = 0

[gmx-users] Re: Average box size

[Navjeet Ahalawat]

Hi Tsjerk,

Thanks for your clarifications. I still couldn't follow how I can calculate
the scaling factor. As I wrote earlier, I ran NPT simulation for equilibration.

Now to start the NVT production run, I need to know the AVERAGE LENGTHS
(a, b, c) of the triclinic box vectors so that I can generate the
triclinic box with the
help of the corresponding angles (88.30, 107.40, 112.20) using the
command "editconf".

Now I understand that the box-x, box-y, and box-z represents the diagonal
elements of triangular matrix and the average volume of my triclinic box
is the product of these diagonal elements. However, as I understand the
command "editconf" requires the length of the box vectors and the three angles
to create a triclinic box.

I would greatly appreciate if you could please let me know the command(s) that
I would require to use to achieve my goal.




Message: 4
Date: Tue, 4 Jan 2011 12:35:36 +0100
From: Tsjerk Wassenaar 
Subject: Re: [gmx-users] Re: Average box size
To: Discussion list for GROMACS users 
Message-ID:
       
Content-Type: text/plain; charset=ISO-8859-1

Hi Navjeet,

These you had in the log file as you showed in your mail. Note that
you use isotropic pressure coupling, so you just need to calculate a
scaling factor, which you can give to editconf to change your system
to match the average box size.

 Cheers,

Tsjerk

On Tue, Jan 4, 2011 at 12:03 PM, Navjeet Ahalawat  wrote:
> Hi Tsjerk,
>
> Thanks for reply, Please can you tell me how can I get the average box
> length (a b c) of my triclinic box for my next step.
>
>> Message: 2
>> Date: Mon, 3 Jan 2011 18:17:15 +0100
>> From: Tsjerk Wassenaar 
>> Subject: Re: [gmx-users] Average box size
>> To: Discussion list for GROMACS users 
>> Message-ID:
>>        
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Hi Navjeet,
>>
>> The box is defined as a triangular matrix, so the volume equals the product
>> of the diagonal elements.
>>
>> Hope it helps,
>>
>> Tsjerk
>>
>> On Jan 3, 2011 5:57 PM, "Navjeet Ahalawat"  wrote:
>>
>> Hi all
>>
>> I did NPT simulation for 30 ns using triclinic box (-angles 88.30,
>> 107.40, 112.20) and Isotropic pressure coupling. Now i want to use
>> average box size for production run (NVT). But I am confused because i
>> am not able to get the meaning of the output values of the log file.
>>
>>
>> Log file output.
>>
>>       <==  ###  ==>
>>       <  A V E R A G E S  >
>>       <==  ###  ==>
>>
>>  Energies (kJ/mol)
>>          Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>>   9.31715e+02    2.35558e+03    1.63083e+02    5.15266e+03    1.79003e+03
>>    Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
>>   1.63211e+04    2.86765e+04   -1.72320e+05   -4.98704e+04   -1.66800e+05
>>   Kinetic En.   Total Energy    Temperature Pressure (bar)  Cons. rmsd ()
>>   1.27874e+04   -1.54012e+05    1.49958e+02    1.07033e+00    0.0e+00
>>
>>         Box-X          Box-Y          Box-Z         Volume   Density (SI)
>>   4.44479e+00    4.49781e+00    4.88259e+00    9.76118e+01    1.04364e+03
>>
>> If Box-X Box-Y Box-Z represent average value of  a b c then volume
>> does not correspond to my triclinic box because its just
>> multiplication of Box-X Box-Y Box-Z. So Please can anybody help me
>> which volume should I consider for next NVT production run.
>>
>> Any help in this regard would be highly appreciated.
>>
>>
>> Thanks & Regards,
>> Navjeet Ahalawat
> --
> gmx-users mailing list    gmx-us...@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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> www interface or send it to gmx-users-requ...@gromacs.org.
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>

--
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands


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Re: [gmx-users] percentage of secondary structure

[Justin A. Lemkul]

ahmet yıldırım wrote:
I get the residue versus time ( secondary structure graph) using do_dssp 
tool. I want to get the percentage value(alpha helix, beta sheet, coil 
...) of secondary structure. For example:


Secondary structure percentage (%):
Helix:51.6
B-sheet:0
Random coil:24.0
Turn:24.4


Have a look at the other output file do_dssp gives you.

-Justin



04 Ocak 2011 14:59 tarihinde Mark Abraham > yazdı:


On 4/01/2011 11:38 PM, ahmet yıldırım wrote:

Dear Mark,

I will do by using the g_analyze tool but I do not know how to use it.


There's a section in Appendix D of the manual for each tool, or you
can use the -h argument to the tool to get the same information.

Either way, you haven't got the right tool. Hint: it's a "protein
specific analysis"

Mark




Thanks

2011/1/4 Mark Abraham mailto:mark.abra...@anu.edu.au>>

On 4/01/2011 8:33 PM, ahmet yıldırım wrote:

Hi,

How can I calculate the percentages (alpha helix, beta
sheet, coil ...) of secondary structure?


Look in manual section 7.4 for a suitable tool.

Mark
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-- 
Ahmet YILDIRIM



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--
Ahmet YILDIRIM



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] percentage of secondary structure

[Thomas Evangelidis]

This is the way to do it with Pymol for one frame:

http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg08154.html

I guess with a little bit of python scripting you could read through all the
frames of your trajectory.

Thomas


2011/1/4 ahmet yıldırım 

> I get the residue versus time ( secondary structure graph) using do_dssp
> tool. I want to get the percentage value(alpha helix, beta sheet, coil ...)
> of secondary structure. For example:
>
> Secondary structure percentage (%):
> Helix:51.6
> B-sheet:0
> Random coil:24.0
> Turn:24.4
>
> 04 Ocak 2011 14:59 tarihinde Mark Abraham  yazdı:
>
>>  On 4/01/2011 11:38 PM, ahmet yıldırım wrote:
>>
>> Dear Mark,
>>
>> I will do by using the g_analyze tool but I do not know how to use it.
>>
>>
>> There's a section in Appendix D of the manual for each tool, or you can
>> use the -h argument to the tool to get the same information.
>>
>> Either way, you haven't got the right tool. Hint: it's a "protein specific
>> analysis"
>>
>> Mark
>>
>>
>>
>> Thanks
>>
>>  2011/1/4 Mark Abraham 
>>
>>> On 4/01/2011 8:33 PM, ahmet yıldırım wrote:
>>>
 Hi,

 How can I calculate the percentages (alpha helix, beta sheet, coil ...)
 of secondary structure?

>>>
>>>  Look in manual section 7.4 for a suitable tool.
>>>
>>> Mark
>>>  --
>>> 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!
>>> Please don't post (un)subscribe requests to the list. Use the www
>>> interface or send it to gmx-users-requ...@gromacs.org.
>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>
>>
>>
>> --
>> Ahmet YILDIRIM
>>
>>
>>
>> --
>>
>> 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!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
> --
> Ahmet YILDIRIM
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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Re: [gmx-users] percentage of secondary structure

[ahmet yıldırım]

I get the residue versus time ( secondary structure graph) using do_dssp
tool. I want to get the percentage value(alpha helix, beta sheet, coil ...)
of secondary structure. For example:

Secondary structure percentage (%):
Helix:51.6
B-sheet:0
Random coil:24.0
Turn:24.4

04 Ocak 2011 14:59 tarihinde Mark Abraham  yazdı:

>  On 4/01/2011 11:38 PM, ahmet yıldırım wrote:
>
> Dear Mark,
>
> I will do by using the g_analyze tool but I do not know how to use it.
>
>
> There's a section in Appendix D of the manual for each tool, or you can use
> the -h argument to the tool to get the same information.
>
> Either way, you haven't got the right tool. Hint: it's a "protein specific
> analysis"
>
> Mark
>
>
>
> Thanks
>
>  2011/1/4 Mark Abraham 
>
>> On 4/01/2011 8:33 PM, ahmet yıldırım wrote:
>>
>>> Hi,
>>>
>>> How can I calculate the percentages (alpha helix, beta sheet, coil ...)
>>> of secondary structure?
>>>
>>
>>  Look in manual section 7.4 for a suitable tool.
>>
>> Mark
>>  --
>> gmx-users mailing listgmx-users@gromacs.org
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>
>
>
> --
> Ahmet YILDIRIM
>
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] percentage of secondary structure

[Mark Abraham]

On 4/01/2011 11:38 PM, ahmet yıldırım wrote:

Dear Mark,

I will do by using the g_analyze tool but I do not know how to use it.


There's a section in Appendix D of the manual for each tool, or you can 
use the -h argument to the tool to get the same information.


Either way, you haven't got the right tool. Hint: it's a "protein 
specific analysis"


Mark



Thanks

2011/1/4 Mark Abraham >


On 4/01/2011 8:33 PM, ahmet yıldırım wrote:

Hi,

How can I calculate the percentages (alpha helix, beta sheet,
coil ...) of secondary structure?


Look in manual section 7.4 for a suitable tool.

Mark
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Re: [gmx-users] percentage of secondary structure

[ahmet yıldırım]

Dear Mark,

I will do by using the g_analyze tool but I do not know how to use it.

Thanks

2011/1/4 Mark Abraham 

> On 4/01/2011 8:33 PM, ahmet yıldırım wrote:
>
>> Hi,
>>
>> How can I calculate the percentages (alpha helix, beta sheet, coil ...) of
>> secondary structure?
>>
>
> Look in manual section 7.4 for a suitable tool.
>
> Mark
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] Re: Average box size

[Tsjerk Wassenaar]

Hi Navjeet,

These you had in the log file as you showed in your mail. Note that
you use isotropic pressure coupling, so you just need to calculate a
scaling factor, which you can give to editconf to change your system
to match the average box size.

 Cheers,

Tsjerk

On Tue, Jan 4, 2011 at 12:03 PM, Navjeet Ahalawat  wrote:
> Hi Tsjerk,
>
> Thanks for reply, Please can you tell me how can I get the average box
> length (a b c) of my triclinic box for my next step.
>
>> Message: 2
>> Date: Mon, 3 Jan 2011 18:17:15 +0100
>> From: Tsjerk Wassenaar 
>> Subject: Re: [gmx-users] Average box size
>> To: Discussion list for GROMACS users 
>> Message-ID:
>>        
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Hi Navjeet,
>>
>> The box is defined as a triangular matrix, so the volume equals the product
>> of the diagonal elements.
>>
>> Hope it helps,
>>
>> Tsjerk
>>
>> On Jan 3, 2011 5:57 PM, "Navjeet Ahalawat"  wrote:
>>
>> Hi all
>>
>> I did NPT simulation for 30 ns using triclinic box (-angles 88.30,
>> 107.40, 112.20) and Isotropic pressure coupling. Now i want to use
>> average box size for production run (NVT). But I am confused because i
>> am not able to get the meaning of the output values of the log file.
>>
>>
>> Log file output.
>>
>>       <==  ###  ==>
>>       <  A V E R A G E S  >
>>       <==  ###  ==>
>>
>>  Energies (kJ/mol)
>>          Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>>   9.31715e+02    2.35558e+03    1.63083e+02    5.15266e+03    1.79003e+03
>>    Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
>>   1.63211e+04    2.86765e+04   -1.72320e+05   -4.98704e+04   -1.66800e+05
>>   Kinetic En.   Total Energy    Temperature Pressure (bar)  Cons. rmsd ()
>>   1.27874e+04   -1.54012e+05    1.49958e+02    1.07033e+00    0.0e+00
>>
>>         Box-X          Box-Y          Box-Z         Volume   Density (SI)
>>   4.44479e+00    4.49781e+00    4.88259e+00    9.76118e+01    1.04364e+03
>>
>> If Box-X Box-Y Box-Z represent average value of  a b c then volume
>> does not correspond to my triclinic box because its just
>> multiplication of Box-X Box-Y Box-Z. So Please can anybody help me
>> which volume should I consider for next NVT production run.
>>
>> Any help in this regard would be highly appreciated.
>>
>>
>> Thanks & Regards,
>> Navjeet Ahalawat
> --
> gmx-users mailing list    gmx-us...@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] percentage of secondary structure

[Mark Abraham]

On 4/01/2011 8:33 PM, ahmet yıldırım wrote:

Hi,

How can I calculate the percentages (alpha helix, beta sheet, coil 
...) of secondary structure?


Look in manual section 7.4 for a suitable tool.

Mark
--
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Re: [gmx-users] Trifluoroethanol-Ethanol mixtures study

[Mark Abraham]

On 4/01/2011 9:55 PM, Marcelo Silva wrote:

Thank you Mark,

But in the case of trifluoroethanol:

C(F)   0.53231
F   -0.20571
F   -0.20571
F   -0.20571
C(H)   0.12632
H(C)   0.08252
H(C)   0.08252
O   -0.63512
H0.42862

The total charge is zero, but if we take the same pattern as for 
ethanol, the charge group 1, for example, don't add to zero.


OK, so what did the author of these charges have to say about that, and 
in what manner did they intend to use it? Did their observations justify 
their parameters?


In the manual it says "When all chemical moieties have a net charge 
ofzero, these jumps can be reduced by moving groups of atoms with net 
charge zero, called charge groups, in and out of the neighbor list", 
that's why I have this question.


There's am unspoken caveat there that this is important when using an 
electrostatics method that only treats the atoms that are in the 
neighbour list. With PME, this question becomes moot.


Mark
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[gmx-users] Re: Average box size

[Navjeet Ahalawat]

Hi Tsjerk,

Thanks for reply, Please can you tell me how can I get the average box
length (a b c) of my triclinic box for my next step.

> Message: 2
> Date: Mon, 3 Jan 2011 18:17:15 +0100
> From: Tsjerk Wassenaar 
> Subject: Re: [gmx-users] Average box size
> To: Discussion list for GROMACS users 
> Message-ID:
>        
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Navjeet,
>
> The box is defined as a triangular matrix, so the volume equals the product
> of the diagonal elements.
>
> Hope it helps,
>
> Tsjerk
>
> On Jan 3, 2011 5:57 PM, "Navjeet Ahalawat"  wrote:
>
> Hi all
>
> I did NPT simulation for 30 ns using triclinic box (-angles 88.30,
> 107.40, 112.20) and Isotropic pressure coupling. Now i want to use
> average box size for production run (NVT). But I am confused because i
> am not able to get the meaning of the output values of the log file.
>
>
> Log file output.
>
>       <==  ###  ==>
>       <  A V E R A G E S  >
>       <==  ###  ==>
>
>  Energies (kJ/mol)
>          Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>   9.31715e+02    2.35558e+03    1.63083e+02    5.15266e+03    1.79003e+03
>    Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
>   1.63211e+04    2.86765e+04   -1.72320e+05   -4.98704e+04   -1.66800e+05
>   Kinetic En.   Total Energy    Temperature Pressure (bar)  Cons. rmsd ()
>   1.27874e+04   -1.54012e+05    1.49958e+02    1.07033e+00    0.0e+00
>
>         Box-X          Box-Y          Box-Z         Volume   Density (SI)
>   4.44479e+00    4.49781e+00    4.88259e+00    9.76118e+01    1.04364e+03
>
> If Box-X Box-Y Box-Z represent average value of  a b c then volume
> does not correspond to my triclinic box because its just
> multiplication of Box-X Box-Y Box-Z. So Please can anybody help me
> which volume should I consider for next NVT production run.
>
> Any help in this regard would be highly appreciated.
>
>
> Thanks & Regards,
> Navjeet Ahalawat
--
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Re: [gmx-users] Trifluoroethanol-Ethanol mixtures study

[Marcelo Silva]

Thank you Mark,

But in the case of trifluoroethanol:

C(F)   0.53231
F   -0.20571
F   -0.20571
F   -0.20571
C(H)   0.12632
H(C)   0.08252
H(C)   0.08252
O   -0.63512
H0.42862

The total charge is zero, but if we take the same pattern as for 
ethanol, the charge group 1, for example, don't add to zero.
In the manual it says "When all chemical moieties have a net charge 
ofzero, these jumps can be reduced by moving groups of atoms with net 
charge zero, called charge groups, in and out of the neighbor list", 
that's why I have this question.


Best regards
--
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Re: [gmx-users] so difficult problem

[Amit Choubey]

Could you post the exact command lines ?

On Tue, Jan 4, 2011 at 1:38 AM, mohsen ramezanpour <
ramezanpour.moh...@gmail.com> wrote:

> please let me know more.
> I am new with gromacs.
> did I understand correctly?You say me to use from trjconv at first and then
> from editconf?
>  I want to keep fix my molecule and rotate my box to locate in awanted
> direction.
> waht can I do?
> because when I rotate the box my molecule totally is located out of box,but
> protein and ligand are connected as the first state and I think my molecule
> has not broken.
> Thanks in advance
>
>
> On Tue, Jan 4, 2011 at 12:56 PM, Amit Choubey  wrote:
>
>> May be you broke the molecule while using editconf. Try to fix the
>> periodicity by trjconv and then use it.
>>
>>
>> On Tue, Jan 4, 2011 at 1:14 AM, mohsen ramezanpour <
>> ramezanpour.moh...@gmail.com> wrote:
>>
>>> I generated my .top and .gro file as drug/enzyme tutorial.
>>> I used PRODRG to generate them.
>>> I could pass all of steps in UMbrella sampling tutorial with these
>>> files,without any warning or error.
>>> the one thing I changed is rotating box with editconf.
>>>
>>>
>>>
>>>
>>> On Tue, Jan 4, 2011 at 12:38 PM, Amit Choubey wrote:
>>>
 There is something wrong with your initial configuration. May be you
 forgot to take care of periodicity, how did you get your initial
 configuration? Also notice that these kind of problems have been discussed
 previously.

 Amit

 On Tue, Jan 4, 2011 at 12:33 AM, mohsen ramezanpour <
 ramezanpour.moh...@gmail.com> wrote:

> Dear All
> I am using this .mdp file and I recived the below warnings,I can't
> solve that.
>
>
> title= NPT
> define   =
> integrator   = md
> tinit= 0
> dt   = 0.002
> nsteps   = 50
> nstcomm  = 1
> comm-grps= protein non-protein
> niter= 20
> nstxout  = 5000
> nstvout  = 5000
> nstfout  = 0
> nstlog   = 5000
> nstenergy= 250
> nstxtcout= 250
> xtc-precision= 1000
> xtc_grps = protein non-protein
> energygrps   = Protein  non-protein
> nstlist  = 5
> ns_type  = grid
> pbc  = xyz
> rlist= 1.4
> domain-decomposition = no
> coulombtype  = PME
> rcoulomb-switch  = 0
> rcoulomb = 1.4
> epsilon-r= 1
> vdw-type = Cut-off
> rvdw-switch  = 0
> rvdw = 1.4
> DispCorr = EnerPres
> fourierspacing   = 0.12
> fourier_nx   = 0
> fourier_ny   = 0
> fourier_nz   = 0
> pme_order= 4
> ewald_rtol   = 1e-05
> epsilon_surface  = 0
> optimize_fft = no
> tcoupl   = Nose-hoover
> tc-grps  = Protein non-protein
> tau_t= 0.1  0.1
> ref_t= 300  300
> Pcoupl   = Parrinello-Rahman
> Pcoupltype   = Isotropic
> tau_p= 1.0
> compressibility  = 4.5e-5
> ref_p= 1.0
> annealing= no
> gen_vel  = yes
> gen_temp = 310
> gen_seed = 173529
> constraints  = all-bonds
> constraint-algorithm = Lincs
> unconstrained-start  = no
> lincs-order  = 4
> lincs-warnangle  = 30
> morse= no
>
> my sytem is protein-ligand,I want to generate a NPT.
> the result was:
>
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.002537, max 0.119994 (between atoms 5293 and 5294)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
> starting mdrun 'Protein in water'
> 50 steps,   1000.0 ps.
>
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 1503.633433, max 55362.878906 (between atoms 5289 and 5290)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>5264   5263   41.70.1143   0.1261  0.1140
>5293   5294   82.70.1221 2612.9744  0.1090
>5291   5293   77.20.1517 6082.6147  0.1390
>5291   5292  101.00.1117 1518.6106  0.1090
>5289   5291   87.70.1353 6891.8911  0.1390
>5289   5290   88.40.1437 7529.4878   

[gmx-users] Re: gmx-users Digest, Vol 81, Issue 14

[Navjeet Ahalawat]

Hi Tsjerk,

Thanks for reply, Please can you tell me how can I get the average box
length (a b c) of my triclinic box for my next step.

> Message: 2
> Date: Mon, 3 Jan 2011 18:17:15 +0100
> From: Tsjerk Wassenaar 
> Subject: Re: [gmx-users] Average box size
> To: Discussion list for GROMACS users 
> Message-ID:
>        
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Navjeet,
>
> The box is defined as a triangular matrix, so the volume equals the product
> of the diagonal elements.
>
> Hope it helps,
>
> Tsjerk
>
> On Jan 3, 2011 5:57 PM, "Navjeet Ahalawat"  wrote:
>
> Hi all
>
> I did NPT simulation for 30 ns using triclinic box (-angles 88.30,
> 107.40, 112.20) and Isotropic pressure coupling. Now i want to use
> average box size for production run (NVT). But I am confused because i
> am not able to get the meaning of the output values of the log file.
>
>
> Log file output.
>
>       <==  ###  ==>
>       <  A V E R A G E S  >
>       <==  ###  ==>
>
>  Energies (kJ/mol)
>          Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>   9.31715e+02    2.35558e+03    1.63083e+02    5.15266e+03    1.79003e+03
>    Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
>   1.63211e+04    2.86765e+04   -1.72320e+05   -4.98704e+04   -1.66800e+05
>   Kinetic En.   Total Energy    Temperature Pressure (bar)  Cons. rmsd ()
>   1.27874e+04   -1.54012e+05    1.49958e+02    1.07033e+00    0.0e+00
>
>         Box-X          Box-Y          Box-Z         Volume   Density (SI)
>   4.44479e+00    4.49781e+00    4.88259e+00    9.76118e+01    1.04364e+03
>
> If Box-X Box-Y Box-Z represent average value of  a b c then volume
> does not correspond to my triclinic box because its just
> multiplication of Box-X Box-Y Box-Z. So Please can anybody help me
> which volume should I consider for next NVT production run.
>
> Any help in this regard would be highly appreciated.
>
>
> Thanks & Regards,
> Navjeet Ahalawat
--
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!
Please don't post (un)subscribe requests to the list. Use the
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Re: [gmx-users] so difficult problem

[mohsen ramezanpour]

please let me know more.
I am new with gromacs.
did I understand correctly?You say me to use from trjconv at first and then
from editconf?
 I want to keep fix my molecule and rotate my box to locate in awanted
direction.
waht can I do?
because when I rotate the box my molecule totally is located out of box,but
protein and ligand are connected as the first state and I think my molecule
has not broken.
Thanks in advance

On Tue, Jan 4, 2011 at 12:56 PM, Amit Choubey  wrote:

> May be you broke the molecule while using editconf. Try to fix the
> periodicity by trjconv and then use it.
>
>
> On Tue, Jan 4, 2011 at 1:14 AM, mohsen ramezanpour <
> ramezanpour.moh...@gmail.com> wrote:
>
>> I generated my .top and .gro file as drug/enzyme tutorial.
>> I used PRODRG to generate them.
>> I could pass all of steps in UMbrella sampling tutorial with these
>> files,without any warning or error.
>> the one thing I changed is rotating box with editconf.
>>
>>
>>
>>
>> On Tue, Jan 4, 2011 at 12:38 PM, Amit Choubey  wrote:
>>
>>> There is something wrong with your initial configuration. May be you
>>> forgot to take care of periodicity, how did you get your initial
>>> configuration? Also notice that these kind of problems have been discussed
>>> previously.
>>>
>>> Amit
>>>
>>> On Tue, Jan 4, 2011 at 12:33 AM, mohsen ramezanpour <
>>> ramezanpour.moh...@gmail.com> wrote:
>>>
 Dear All
 I am using this .mdp file and I recived the below warnings,I can't solve
 that.


 title= NPT
 define   =
 integrator   = md
 tinit= 0
 dt   = 0.002
 nsteps   = 50
 nstcomm  = 1
 comm-grps= protein non-protein
 niter= 20
 nstxout  = 5000
 nstvout  = 5000
 nstfout  = 0
 nstlog   = 5000
 nstenergy= 250
 nstxtcout= 250
 xtc-precision= 1000
 xtc_grps = protein non-protein
 energygrps   = Protein  non-protein
 nstlist  = 5
 ns_type  = grid
 pbc  = xyz
 rlist= 1.4
 domain-decomposition = no
 coulombtype  = PME
 rcoulomb-switch  = 0
 rcoulomb = 1.4
 epsilon-r= 1
 vdw-type = Cut-off
 rvdw-switch  = 0
 rvdw = 1.4
 DispCorr = EnerPres
 fourierspacing   = 0.12
 fourier_nx   = 0
 fourier_ny   = 0
 fourier_nz   = 0
 pme_order= 4
 ewald_rtol   = 1e-05
 epsilon_surface  = 0
 optimize_fft = no
 tcoupl   = Nose-hoover
 tc-grps  = Protein non-protein
 tau_t= 0.1  0.1
 ref_t= 300  300
 Pcoupl   = Parrinello-Rahman
 Pcoupltype   = Isotropic
 tau_p= 1.0
 compressibility  = 4.5e-5
 ref_p= 1.0
 annealing= no
 gen_vel  = yes
 gen_temp = 310
 gen_seed = 173529
 constraints  = all-bonds
 constraint-algorithm = Lincs
 unconstrained-start  = no
 lincs-order  = 4
 lincs-warnangle  = 30
 morse= no

 my sytem is protein-ligand,I want to generate a NPT.
 the result was:

 Step 0, time 0 (ps)  LINCS WARNING
 relative constraint deviation after LINCS:
 rms 0.002537, max 0.119994 (between atoms 5293 and 5294)
 bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
 starting mdrun 'Protein in water'
 50 steps,   1000.0 ps.

 Step 0, time 0 (ps)  LINCS WARNING
 relative constraint deviation after LINCS:
 rms 1503.633433, max 55362.878906 (between atoms 5289 and 5290)
 bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
5264   5263   41.70.1143   0.1261  0.1140
5293   5294   82.70.1221 2612.9744  0.1090
5291   5293   77.20.1517 6082.6147  0.1390
5291   5292  101.00.1117 1518.6106  0.1090
5289   5291   87.70.1353 6891.8911  0.1390
5289   5290   88.40.1437 7529.4878  0.1360
5289   5287   88.40.1456 7540.4873  0.1390
5287   5288   89.70.1092 381.5114  0.1090
5285   5287   92.30.1395 354.9220  0.1390
5285   5286  123.80.1101  44.8448  0.1090
5284   5293   89.00

[gmx-users] percentage of secondary structure

[ahmet yıldırım]

Hi,

How can I calculate the percentages (alpha helix, beta sheet, coil ...) of
secondary structure?

Thanks in advance

-- 
Ahmet YILDIRIM
-- 
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Re: [gmx-users] so difficult problem

[Amit Choubey]

May be you broke the molecule while using editconf. Try to fix the
periodicity by trjconv and then use it.

On Tue, Jan 4, 2011 at 1:14 AM, mohsen ramezanpour <
ramezanpour.moh...@gmail.com> wrote:

> I generated my .top and .gro file as drug/enzyme tutorial.
> I used PRODRG to generate them.
> I could pass all of steps in UMbrella sampling tutorial with these
> files,without any warning or error.
> the one thing I changed is rotating box with editconf.
>
>
>
>
> On Tue, Jan 4, 2011 at 12:38 PM, Amit Choubey  wrote:
>
>> There is something wrong with your initial configuration. May be you
>> forgot to take care of periodicity, how did you get your initial
>> configuration? Also notice that these kind of problems have been discussed
>> previously.
>>
>> Amit
>>
>> On Tue, Jan 4, 2011 at 12:33 AM, mohsen ramezanpour <
>> ramezanpour.moh...@gmail.com> wrote:
>>
>>> Dear All
>>> I am using this .mdp file and I recived the below warnings,I can't solve
>>> that.
>>>
>>>
>>> title= NPT
>>> define   =
>>> integrator   = md
>>> tinit= 0
>>> dt   = 0.002
>>> nsteps   = 50
>>> nstcomm  = 1
>>> comm-grps= protein non-protein
>>> niter= 20
>>> nstxout  = 5000
>>> nstvout  = 5000
>>> nstfout  = 0
>>> nstlog   = 5000
>>> nstenergy= 250
>>> nstxtcout= 250
>>> xtc-precision= 1000
>>> xtc_grps = protein non-protein
>>> energygrps   = Protein  non-protein
>>> nstlist  = 5
>>> ns_type  = grid
>>> pbc  = xyz
>>> rlist= 1.4
>>> domain-decomposition = no
>>> coulombtype  = PME
>>> rcoulomb-switch  = 0
>>> rcoulomb = 1.4
>>> epsilon-r= 1
>>> vdw-type = Cut-off
>>> rvdw-switch  = 0
>>> rvdw = 1.4
>>> DispCorr = EnerPres
>>> fourierspacing   = 0.12
>>> fourier_nx   = 0
>>> fourier_ny   = 0
>>> fourier_nz   = 0
>>> pme_order= 4
>>> ewald_rtol   = 1e-05
>>> epsilon_surface  = 0
>>> optimize_fft = no
>>> tcoupl   = Nose-hoover
>>> tc-grps  = Protein non-protein
>>> tau_t= 0.1  0.1
>>> ref_t= 300  300
>>> Pcoupl   = Parrinello-Rahman
>>> Pcoupltype   = Isotropic
>>> tau_p= 1.0
>>> compressibility  = 4.5e-5
>>> ref_p= 1.0
>>> annealing= no
>>> gen_vel  = yes
>>> gen_temp = 310
>>> gen_seed = 173529
>>> constraints  = all-bonds
>>> constraint-algorithm = Lincs
>>> unconstrained-start  = no
>>> lincs-order  = 4
>>> lincs-warnangle  = 30
>>> morse= no
>>>
>>> my sytem is protein-ligand,I want to generate a NPT.
>>> the result was:
>>>
>>> Step 0, time 0 (ps)  LINCS WARNING
>>> relative constraint deviation after LINCS:
>>> rms 0.002537, max 0.119994 (between atoms 5293 and 5294)
>>> bonds that rotated more than 30 degrees:
>>>  atom 1 atom 2  angle  previous, current, constraint length
>>> starting mdrun 'Protein in water'
>>> 50 steps,   1000.0 ps.
>>>
>>> Step 0, time 0 (ps)  LINCS WARNING
>>> relative constraint deviation after LINCS:
>>> rms 1503.633433, max 55362.878906 (between atoms 5289 and 5290)
>>> bonds that rotated more than 30 degrees:
>>>  atom 1 atom 2  angle  previous, current, constraint length
>>>5264   5263   41.70.1143   0.1261  0.1140
>>>5293   5294   82.70.1221 2612.9744  0.1090
>>>5291   5293   77.20.1517 6082.6147  0.1390
>>>5291   5292  101.00.1117 1518.6106  0.1090
>>>5289   5291   87.70.1353 6891.8911  0.1390
>>>5289   5290   88.40.1437 7529.4878  0.1360
>>>5289   5287   88.40.1456 7540.4873  0.1390
>>>5287   5288   89.70.1092 381.5114  0.1090
>>>5285   5287   92.30.1395 354.9220  0.1390
>>>5285   5286  123.80.1101  44.8448  0.1090
>>>5284   5293   89.00.1478 4605.1763  0.1390
>>>5284   5285   79.30.1402 173.5627  0.1390
>>>5278   5279   78.90.1529   1.1270  0.1530
>>>5277   5278  122.90.1545  13.1423  0.1530
>>>5276   5284   84.90.1422 159.0098  0.1390
>>>5276   5277   68.40.1543  90.8248  0.1530
>>>5276   5275   39.50.1439  72.5216  0.1430
>>>5274   5275  103.70.1436  21.6028  0.1430
>>>5273   5274  108.50.1394   3.3421  0.1390
>>>5276   5272   45.70.1402  80.6795  0.1390
>>>5272   5273  127.30.1340  14.2401  0.1330
>>> 

Re: [gmx-users] so difficult problem

[mohsen ramezanpour]

I generated my .top and .gro file as drug/enzyme tutorial.
I used PRODRG to generate them.
I could pass all of steps in UMbrella sampling tutorial with these
files,without any warning or error.
the one thing I changed is rotating box with editconf.



On Tue, Jan 4, 2011 at 12:38 PM, Amit Choubey  wrote:

> There is something wrong with your initial configuration. May be you forgot
> to take care of periodicity, how did you get your initial configuration?
> Also notice that these kind of problems have been discussed previously.
>
> Amit
>
> On Tue, Jan 4, 2011 at 12:33 AM, mohsen ramezanpour <
> ramezanpour.moh...@gmail.com> wrote:
>
>> Dear All
>> I am using this .mdp file and I recived the below warnings,I can't solve
>> that.
>>
>>
>> title= NPT
>> define   =
>> integrator   = md
>> tinit= 0
>> dt   = 0.002
>> nsteps   = 50
>> nstcomm  = 1
>> comm-grps= protein non-protein
>> niter= 20
>> nstxout  = 5000
>> nstvout  = 5000
>> nstfout  = 0
>> nstlog   = 5000
>> nstenergy= 250
>> nstxtcout= 250
>> xtc-precision= 1000
>> xtc_grps = protein non-protein
>> energygrps   = Protein  non-protein
>> nstlist  = 5
>> ns_type  = grid
>> pbc  = xyz
>> rlist= 1.4
>> domain-decomposition = no
>> coulombtype  = PME
>> rcoulomb-switch  = 0
>> rcoulomb = 1.4
>> epsilon-r= 1
>> vdw-type = Cut-off
>> rvdw-switch  = 0
>> rvdw = 1.4
>> DispCorr = EnerPres
>> fourierspacing   = 0.12
>> fourier_nx   = 0
>> fourier_ny   = 0
>> fourier_nz   = 0
>> pme_order= 4
>> ewald_rtol   = 1e-05
>> epsilon_surface  = 0
>> optimize_fft = no
>> tcoupl   = Nose-hoover
>> tc-grps  = Protein non-protein
>> tau_t= 0.1  0.1
>> ref_t= 300  300
>> Pcoupl   = Parrinello-Rahman
>> Pcoupltype   = Isotropic
>> tau_p= 1.0
>> compressibility  = 4.5e-5
>> ref_p= 1.0
>> annealing= no
>> gen_vel  = yes
>> gen_temp = 310
>> gen_seed = 173529
>> constraints  = all-bonds
>> constraint-algorithm = Lincs
>> unconstrained-start  = no
>> lincs-order  = 4
>> lincs-warnangle  = 30
>> morse= no
>>
>> my sytem is protein-ligand,I want to generate a NPT.
>> the result was:
>>
>> Step 0, time 0 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.002537, max 0.119994 (between atoms 5293 and 5294)
>> bonds that rotated more than 30 degrees:
>>  atom 1 atom 2  angle  previous, current, constraint length
>> starting mdrun 'Protein in water'
>> 50 steps,   1000.0 ps.
>>
>> Step 0, time 0 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 1503.633433, max 55362.878906 (between atoms 5289 and 5290)
>> bonds that rotated more than 30 degrees:
>>  atom 1 atom 2  angle  previous, current, constraint length
>>5264   5263   41.70.1143   0.1261  0.1140
>>5293   5294   82.70.1221 2612.9744  0.1090
>>5291   5293   77.20.1517 6082.6147  0.1390
>>5291   5292  101.00.1117 1518.6106  0.1090
>>5289   5291   87.70.1353 6891.8911  0.1390
>>5289   5290   88.40.1437 7529.4878  0.1360
>>5289   5287   88.40.1456 7540.4873  0.1390
>>5287   5288   89.70.1092 381.5114  0.1090
>>5285   5287   92.30.1395 354.9220  0.1390
>>5285   5286  123.80.1101  44.8448  0.1090
>>5284   5293   89.00.1478 4605.1763  0.1390
>>5284   5285   79.30.1402 173.5627  0.1390
>>5278   5279   78.90.1529   1.1270  0.1530
>>5277   5278  122.90.1545  13.1423  0.1530
>>5276   5284   84.90.1422 159.0098  0.1390
>>5276   5277   68.40.1543  90.8248  0.1530
>>5276   5275   39.50.1439  72.5216  0.1430
>>5274   5275  103.70.1436  21.6028  0.1430
>>5273   5274  108.50.1394   3.3421  0.1390
>>5276   5272   45.70.1402  80.6795  0.1390
>>5272   5273  127.30.1340  14.2401  0.1330
>>5272   5270   69.80.1336  12.6250  0.1330
>>5270   5271  113.30.1092   0.2530  0.1090
>>5268   5270  104.60.1391   0.2718  0.1390
>>5268   5269   44.40.1091   0.1636  0.1090
>>5273   5266   58.50.1342  14.0125  0.1330
>>5265   5268   36.50.1394   0.1769  0.139

Re: [gmx-users] so difficult problem

[Amit Choubey]

There is something wrong with your initial configuration. May be you forgot
to take care of periodicity, how did you get your initial configuration?
Also notice that these kind of problems have been discussed previously.

Amit

On Tue, Jan 4, 2011 at 12:33 AM, mohsen ramezanpour <
ramezanpour.moh...@gmail.com> wrote:

> Dear All
> I am using this .mdp file and I recived the below warnings,I can't solve
> that.
>
>
> title= NPT
> define   =
> integrator   = md
> tinit= 0
> dt   = 0.002
> nsteps   = 50
> nstcomm  = 1
> comm-grps= protein non-protein
> niter= 20
> nstxout  = 5000
> nstvout  = 5000
> nstfout  = 0
> nstlog   = 5000
> nstenergy= 250
> nstxtcout= 250
> xtc-precision= 1000
> xtc_grps = protein non-protein
> energygrps   = Protein  non-protein
> nstlist  = 5
> ns_type  = grid
> pbc  = xyz
> rlist= 1.4
> domain-decomposition = no
> coulombtype  = PME
> rcoulomb-switch  = 0
> rcoulomb = 1.4
> epsilon-r= 1
> vdw-type = Cut-off
> rvdw-switch  = 0
> rvdw = 1.4
> DispCorr = EnerPres
> fourierspacing   = 0.12
> fourier_nx   = 0
> fourier_ny   = 0
> fourier_nz   = 0
> pme_order= 4
> ewald_rtol   = 1e-05
> epsilon_surface  = 0
> optimize_fft = no
> tcoupl   = Nose-hoover
> tc-grps  = Protein non-protein
> tau_t= 0.1  0.1
> ref_t= 300  300
> Pcoupl   = Parrinello-Rahman
> Pcoupltype   = Isotropic
> tau_p= 1.0
> compressibility  = 4.5e-5
> ref_p= 1.0
> annealing= no
> gen_vel  = yes
> gen_temp = 310
> gen_seed = 173529
> constraints  = all-bonds
> constraint-algorithm = Lincs
> unconstrained-start  = no
> lincs-order  = 4
> lincs-warnangle  = 30
> morse= no
>
> my sytem is protein-ligand,I want to generate a NPT.
> the result was:
>
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.002537, max 0.119994 (between atoms 5293 and 5294)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
> starting mdrun 'Protein in water'
> 50 steps,   1000.0 ps.
>
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 1503.633433, max 55362.878906 (between atoms 5289 and 5290)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>5264   5263   41.70.1143   0.1261  0.1140
>5293   5294   82.70.1221 2612.9744  0.1090
>5291   5293   77.20.1517 6082.6147  0.1390
>5291   5292  101.00.1117 1518.6106  0.1090
>5289   5291   87.70.1353 6891.8911  0.1390
>5289   5290   88.40.1437 7529.4878  0.1360
>5289   5287   88.40.1456 7540.4873  0.1390
>5287   5288   89.70.1092 381.5114  0.1090
>5285   5287   92.30.1395 354.9220  0.1390
>5285   5286  123.80.1101  44.8448  0.1090
>5284   5293   89.00.1478 4605.1763  0.1390
>5284   5285   79.30.1402 173.5627  0.1390
>5278   5279   78.90.1529   1.1270  0.1530
>5277   5278  122.90.1545  13.1423  0.1530
>5276   5284   84.90.1422 159.0098  0.1390
>5276   5277   68.40.1543  90.8248  0.1530
>5276   5275   39.50.1439  72.5216  0.1430
>5274   5275  103.70.1436  21.6028  0.1430
>5273   5274  108.50.1394   3.3421  0.1390
>5276   5272   45.70.1402  80.6795  0.1390
>5272   5273  127.30.1340  14.2401  0.1330
>5272   5270   69.80.1336  12.6250  0.1330
>5270   5271  113.30.1092   0.2530  0.1090
>5268   5270  104.60.1391   0.2718  0.1390
>5268   5269   44.40.1091   0.1636  0.1090
>5273   5266   58.50.1342  14.0125  0.1330
>5265   5268   36.50.1394   0.1769  0.1390
>
> Back Off! I just backed up step0b.pdb to ./#step0b.pdb.2#
>
> Back Off! I just backed up step0c.pdb to ./#step0c.pdb.2#
> Wrote pdb files with previous and current coordinates
> step 0Warning: 1-4 interaction between 5264 and 5273 at distance 13.965
> 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 inc

[gmx-users] so difficult problem

[mohsen ramezanpour]

Dear All
I am using this .mdp file and I recived the below warnings,I can't solve
that.


title= NPT
define   =
integrator   = md
tinit= 0
dt   = 0.002
nsteps   = 50
nstcomm  = 1
comm-grps= protein non-protein
niter= 20
nstxout  = 5000
nstvout  = 5000
nstfout  = 0
nstlog   = 5000
nstenergy= 250
nstxtcout= 250
xtc-precision= 1000
xtc_grps = protein non-protein
energygrps   = Protein  non-protein
nstlist  = 5
ns_type  = grid
pbc  = xyz
rlist= 1.4
domain-decomposition = no
coulombtype  = PME
rcoulomb-switch  = 0
rcoulomb = 1.4
epsilon-r= 1
vdw-type = Cut-off
rvdw-switch  = 0
rvdw = 1.4
DispCorr = EnerPres
fourierspacing   = 0.12
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
pme_order= 4
ewald_rtol   = 1e-05
epsilon_surface  = 0
optimize_fft = no
tcoupl   = Nose-hoover
tc-grps  = Protein non-protein
tau_t= 0.1  0.1
ref_t= 300  300
Pcoupl   = Parrinello-Rahman
Pcoupltype   = Isotropic
tau_p= 1.0
compressibility  = 4.5e-5
ref_p= 1.0
annealing= no
gen_vel  = yes
gen_temp = 310
gen_seed = 173529
constraints  = all-bonds
constraint-algorithm = Lincs
unconstrained-start  = no
lincs-order  = 4
lincs-warnangle  = 30
morse= no

my sytem is protein-ligand,I want to generate a NPT.
the result was:

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.002537, max 0.119994 (between atoms 5293 and 5294)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
starting mdrun 'Protein in water'
50 steps,   1000.0 ps.

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 1503.633433, max 55362.878906 (between atoms 5289 and 5290)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   5264   5263   41.70.1143   0.1261  0.1140
   5293   5294   82.70.1221 2612.9744  0.1090
   5291   5293   77.20.1517 6082.6147  0.1390
   5291   5292  101.00.1117 1518.6106  0.1090
   5289   5291   87.70.1353 6891.8911  0.1390
   5289   5290   88.40.1437 7529.4878  0.1360
   5289   5287   88.40.1456 7540.4873  0.1390
   5287   5288   89.70.1092 381.5114  0.1090
   5285   5287   92.30.1395 354.9220  0.1390
   5285   5286  123.80.1101  44.8448  0.1090
   5284   5293   89.00.1478 4605.1763  0.1390
   5284   5285   79.30.1402 173.5627  0.1390
   5278   5279   78.90.1529   1.1270  0.1530
   5277   5278  122.90.1545  13.1423  0.1530
   5276   5284   84.90.1422 159.0098  0.1390
   5276   5277   68.40.1543  90.8248  0.1530
   5276   5275   39.50.1439  72.5216  0.1430
   5274   5275  103.70.1436  21.6028  0.1430
   5273   5274  108.50.1394   3.3421  0.1390
   5276   5272   45.70.1402  80.6795  0.1390
   5272   5273  127.30.1340  14.2401  0.1330
   5272   5270   69.80.1336  12.6250  0.1330
   5270   5271  113.30.1092   0.2530  0.1090
   5268   5270  104.60.1391   0.2718  0.1390
   5268   5269   44.40.1091   0.1636  0.1090
   5273   5266   58.50.1342  14.0125  0.1330
   5265   5268   36.50.1394   0.1769  0.1390

Back Off! I just backed up step0b.pdb to ./#step0b.pdb.2#

Back Off! I just backed up step0c.pdb to ./#step0c.pdb.2#
Wrote pdb files with previous and current coordinates
step 0Warning: 1-4 interaction between 5264 and 5273 at distance 13.965
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

Please let me know the solution.
Thanks in advance
-- 
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Re: [gmx-users] How to get sufactant.gro, sufactant.top,

[Mark Abraham]

On 01/04/11, gromacs   wrote:
> Hi expert,
> 
>  
> 
> I'd like to add sufactant to water. That means i should first get the 
> sufactant.gro, and sufactant.top.
> 
> 

No, you need a coordinate file for the starting point for your GROMACS work, 
and the pieces to combine into a .top. That might mean a coordinate file of all 
your surfactant molecules and matching .top file that you then solvate with 
genbox. Or you might want to use genconf to replicate some existing coordinate 
file somehow. Or you might have your starting point already and need to match a 
.top to it.
 

> 
> Someone said that we cannot get sufactant.gro and sufactant.top through 
> grompp ()  sufactant.pdb. Because grompp  .pdb could mainly use for 
> macro-biology big moleculars, which means some proteins etc.
> 
> 

Well they (or your account of them) is wrong on what might be several points. 
Someone needs to understand GROMACS workflows better - perhaps by doing some 
tutorial material and/or reading 
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation


> 
> 
> So that means we could not get correct  .gro, .top small molecules such as 
> inorganic or small organic molecules (such as ethanol).
> 
>  
> 
> So how can we get the sufactant.gro, sufactant.top?
> 
> 

That varies widely with what raw materials exist and what the objective is.


>  and which force field should we choose for ordinary simulation? I know we 
> often use ffoplass force field for solution.
> 
> 

That's your homework, I'm afraid. See above link.

Mark


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