[gmx-users] Artificial Shear Flow and Inconsistent Shift Error

[He, Yang]

Hi All,

1. Artificial Shear Flow: I am trying to do translocation studies and wanted to 
generate a shear flow without actual water atoms. I checked the mail list and 
it was mentioned that there is no velocity profile but an option to accelerate 
the atoms in a group. But I wanted to get the shear flow or the velocity 
profile without atoms.

To make myself clear: I want the boat to navigate through water, with the flow 
of water but there is no water, am I making sense? So I want an artificial 
force applied constantly in the channel not on the particle so basically I 
define the velocity profile using the artificial force.

2. Inconsistent Shifts Error: I received this error in my simulation studies 
when I used PBC =xyz " There were XXX inconsistent shifts. Check your topology 
", checked the mail-list and found the option of pbc = full should be used, but 
seems it is not available anymore in gromacs 4.0.3, My system is very small 
around 1000 atoms, and it works fine without periodic conditions, but when pbc 
is added it runs for some time and then gives me the error.

What does this error actually mean?

How can I resolve this?

Regards,

Aby
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RE: [gmx-users] PME on BlueGene

[He, Yang]

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Mark Abraham [mark.abra...@anu.edu.au]
Sent: Tuesday, June 02, 2009 7:55 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] PME on BlueGene

Jakob Wohlert wrote:
> Hi,
>
> I'm trying to compile Gromacs 4.0.4 for BlueGene/P, and using the
> configuration options from the wiki I have succeeded insofar that I have a
> working program as long as I don't use PME.
>
> I have tried many different variants of fftw - 2.1.5, 3.2.1, single
> precision, double precision, different compiler optimizations and so on,
> but it all ends the same: mdrun getting stuck somewhere in the
> initialization process.
>
> However, by using the built in fft library FFTPACK instead of FFTW, PME
> will work, but that is not really an alternative.
>
> In at least a few cases I have been able to pinpoint the location where it
> hangs - it's in pme.c, subroutine pme_dd_sendrecv. The program calls
> MPI_Sendrecv, but then nothing else happens as far as I can tell.
>
> I'm confused and I have sort of ran out of ideas right now. Has anyone
> else encountered a problem like this, or has anyone any suggestions how to
> proceed from here?

That looks to me like the separate PME nodes are dying through some
linking problem and the problem is only manifest on node 0 when its
sendrecv doesn't complete. Forcing mdrun -npme 0 may confirm this when
all the nodes die at the first point they refer to a symbol in the FFT
library.

Otherwise, looking at warnings/errors from the linker will be required.
Are you compiling an FFT library version for the back end, or the front end?

Mark
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[gmx-users] how to apply shear force

[He, Yang]

Hi all users,

I am wondering how I can apply the shear force into the gromacs .Does anyone 
has such experoence about that?

Really appreciate any suggestions.

Yang
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[gmx-users] how to add shear force in gromacs

[He, Yang]

Hi all users,

I just wonder how  I  can add the shear force in gromacs. I have checked the 
manual but failed to find some effective ways to do that.

Any suggestions will be highly appreciated.

Thank you very much.

Yang
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RE: [gmx-users] input the .gro and .trr file to the VMD

[He, Yang]

HI Mark,

I am indeed using the coarse-graining atoms .What do you mean by " tell
VMD to use suitable rules, or something similar." Do you have any fixed case 
about how to solve this problem in vmd?

Thank you very much.

Yang

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
Of Mark Abraham [mark.abra...@anu.edu.au]
Sent: Monday, April 27, 2009 7:00 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] input the .gro and .trr file to the VMD

He, Yang wrote:
> Hi all users,
>
> I want to get some snap shots from VMD through inputing my gro and trr file 
> to  the VMD. But I always find that I can not get the bond connection among 
> the atoms and then, I try to use the dynamic bonds to solve this problem but  
> another problem is that  when I define a value for the cutoff distance, the 
> bonds which don't exist among the atoms in the original shape will also come 
> up .

VMD guess at bonds based on atom names and inter-atomic distances, so
your .gro file isn't following the rules it expects. Either your
structures are broken, or they're coarse-grained and you need to tell
VMD to use suitable rules, or something similar.

Mark

> Except the dynamic method to figure out this problem, I wonder whether there 
> are other ways to fix this problem.
>
> Thank you for any suggestions.
>
> Yang
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[gmx-users] input the .gro and .trr file to the VMD

[He, Yang]

Hi all users,

I want to get some snap shots from VMD through inputing my gro and trr file to  
the VMD. But I always find that I can not get the bond connection among the 
atoms and then, I try to use the dynamic bonds to solve this problem but  
another problem is that  when I define a value for the cutoff distance, the 
bonds which don't exist among the atoms in the original shape will also come up 
.

Except the dynamic method to figure out this problem, I wonder whether there 
are other ways to fix this problem.

Thank you for any suggestions.

Yang
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RE: [gmx-users] XTC.error

[He, Yang]

Hi,

I also tried the energy minimization but it seems not to work. In fact, when I 
run a similar case like this(just including some DNA single strand) ,it is 
going on well but after I increase some more single DNA strand to the system  
it just show such error.

Yang

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
Of David van der Spoel [sp...@xray.bmc.uu.se]
Sent: Sunday, April 26, 2009 12:13 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] XTC.error

He, Yang wrote:
> Hi all users,
>
> When I run the mdrun command, it always shows that XTC.error. Then I check 
> the md.log file and find that:
>
> There are 220 atoms in your xtc output selection

220 atoms and 3.9e5 bond energy: that is roughly 2000 kJ/mol per bond,
indicating that bonds on average have been elongated by 1 angstrom.
Seems your structure is not good...
Try minimizing. And note that gromacs uses nm, in case you have
generated your own input...

>Energies (kJ/mol)
>Bond   G96AngleProper Dih.LJ (SR)   Coulomb (SR)
> 3.91620e+059.58742e+031.93313e+04   -1.12241e+010.0e+00
>   PotentialKinetic En.   Total EnergyTemperature Pressure (bar)
> 4.20528e+05nannannan0.0e+00
>
> ---
> Program mdrun, VERSION 3.3.1
> Source code file: stat.c, line: 257
>
> Fatal error:
> XTC error
>
> The total energy is shown"nan" I also checked my gro file but there are no 
> lapped atoms. And when I run the command "grompp", there is no any warnings.
>
> Can anybody tell me what is the problem about this error?
>
> Thank you very much.
>
> Yang
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--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se
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[gmx-users] XTC.error

[He, Yang]

Hi all users,

When I run the mdrun command, it always shows that XTC.error. Then I check the 
md.log file and find that:

There are 220 atoms in your xtc output selection
   Energies (kJ/mol)
   Bond   G96AngleProper Dih.LJ (SR)   Coulomb (SR)
3.91620e+059.58742e+031.93313e+04   -1.12241e+010.0e+00
  PotentialKinetic En.   Total EnergyTemperature Pressure (bar)
4.20528e+05nannannan0.0e+00

---
Program mdrun, VERSION 3.3.1
Source code file: stat.c, line: 257

Fatal error:
XTC error

The total energy is shown"nan" I also checked my gro file but there are no 
lapped atoms. And when I run the command "grompp", there is no any warnings.

Can anybody tell me what is the problem about this error?

Thank you very much.

Yang
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RE: [gmx-users] about the bond connection between different groups

[He, Yang]

Hi Tsjerk,

 Thank you very much for your introduction about how to merge two 
moleculetypes. I just follow your instructions as listed below;

I have two moleculetypes named DNA and ICE. This is what I include in topology 
file:


#include "dna.itp"
#include "ICE.itp"

[ moleculetype ]

; molnamecylind

  DNA+ICE  1

[ atoms ]
;   nr  type resnr   res  atom  cgnrcharge  mass
 1bA 1   DNAbA 1  0 178.0
 ...

 20lA 1   ICElA20  0 134.0

[ angles ]
 ...
[ dihedrals ]
 ...
[ system ]
; Name
CGMD

[ molecules ]
; Compound  #mols
DNA+ICE 1

I have 19 atoms in DNA and only one atom in ICE.

Also, I have consider adding the angles and dihedrals involved in the 
interaction. Then, I also include individual itp file for the DNA and ICE 
,respectively .

In addition , I want to freeze the atom in ICE and that is what I include in 
.mdp file :

energygrp_excl  = ICE ICE

;   Non-equilibrium MD
;
freezegrps  =ICE
freezedim   = Y Y Y

[ system ]
; Name
CGMD

[ molecules ]
; Compound  #mols
DNA+ICE 1

But when I run this, it shows that:
"Group ICE not found in indexfile.
Maybe you have non-default goups in your mdp file, while not using the '-n' 
option of grompp.
In that case use the '-n' option."

Can you tell me what is the problem? Thank you for your suggestions.

Regards,

Yang

___
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
Of Tsjerk Wassenaar [tsje...@gmail.com]
Sent: Wednesday, April 22, 2009 11:53 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] about the bond connection between different groups

You have:

[ moleculetype ]
A
[atoms]
1
...
N

and

[ moleculetype ]
B
[atoms]
1
...
M

and want to make a bond between atom X of A and Y of B. So you have to
merge A and B into:

[ moleculetype ]
A+B
[atoms]
1
...
N
N+1
...
N+M

with a.o.:

[bonds]
X Y+N type bond-parameters.

I hope this is clear enough. If it isn't, read Chapter 5 of the manual
thoroughly.

Cheers,

Tsjerk


On Wed, Apr 22, 2009 at 5:30 PM, He, Yang  wrote:
> Hi Tsjerk,
>
> Thank you for your reply. SO you mean I can just define the bond in one 
> moleculetype.As what you said, I have to renumber all atoms from one of the 
> moleculetypes,
> starting at N+1, with N being the number of the last atom of the first 
> moleculetype .Then I wonder  which molecule type the atom N+1 belongs to . 
> Also, I wonder how to define the new atom N+1's moleculetype  in the gro file 
> . I just am not sure about that. Can you give me much more information about 
> that?
>
> Thank you very much.
>
> Yang
> 
> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
> Of Tsjerk Wassenaar [tsje...@gmail.com]
> Sent: Tuesday, April 21, 2009 11:22 PM
> To: jalem...@vt.edu; Discussion list for GROMACS users
> Subject: Re: [gmx-users] about the bond connection between different groups
>
> Hi He Yang, Justin,
>
>>> You have said bonds between distinct molecules require a merged topology.
>>> Is
>>> there any introduction in the manual or Do you have any example about the
>>> merged topology?
>>>
>>
>> A merged topology contains multiple moleculetype definitions in one
>> topol.top. Discussions are in the archives.
>
> Bonds can only be defined within moleculetypes, not between them. So
> you'll need to combine moleculetypes to create a bond between groups.
> For this you have to renumber all atoms from one of the moleculetypes,
> starting at N+1, with N being the number of the last atom of the first
> moleculetype. You also have to renumber the indices for all other
> blocks ([bonds], [angles], etc...). Then combine the blocks and
> finally add the new bond. If it is a proper bond, you should also
> consider adding the angles and dihedrals involved in the interaction.
> Note again, merging to create a bond does not mean adding multiple
> moleculetypes in one topol.top!
>
> Cheers,
>
> Tsjerk
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
> ___
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RE: [gmx-users] about the bond connection between different groups

[He, Yang]

Hi Tsjerk,

Thank you for your reply. SO you mean I can just define the bond in one 
moleculetype.As what you said, I have to renumber all atoms from one of the 
moleculetypes,
starting at N+1, with N being the number of the last atom of the first 
moleculetype .Then I wonder  which molecule type the atom N+1 belongs to . 
Also, I wonder how to define the new atom N+1's moleculetype  in the gro file . 
I just am not sure about that. Can you give me much more information about that?

Thank you very much.

Yang

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
Of Tsjerk Wassenaar [tsje...@gmail.com]
Sent: Tuesday, April 21, 2009 11:22 PM
To: jalem...@vt.edu; Discussion list for GROMACS users
Subject: Re: [gmx-users] about the bond connection between different groups

Hi He Yang, Justin,

>> You have said bonds between distinct molecules require a merged topology.
>> Is
>> there any introduction in the manual or Do you have any example about the
>> merged topology?
>>
>
> A merged topology contains multiple moleculetype definitions in one
> topol.top. Discussions are in the archives.

Bonds can only be defined within moleculetypes, not between them. So
you'll need to combine moleculetypes to create a bond between groups.
For this you have to renumber all atoms from one of the moleculetypes,
starting at N+1, with N being the number of the last atom of the first
moleculetype. You also have to renumber the indices for all other
blocks ([bonds], [angles], etc...). Then combine the blocks and
finally add the new bond. If it is a proper bond, you should also
consider adding the angles and dihedrals involved in the interaction.
Note again, merging to create a bond does not mean adding multiple
moleculetypes in one topol.top!

Cheers,

Tsjerk

--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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RE: [gmx-users] about the bond connection between different groups

[He, Yang]

Hi Justin,

It seems that I can not fix the fragmentation fault when position restraints is 
added and hence, I just consider using the freezegroup method to make some 
atoms  in a whole group fixed .While the freezegroup seems to just be useful 
for the whole group not applicable to some certain atoms in a whole group, I 
consider defining the atoms I want to fix as an individual group and keep the 
other atoms in a nother group but still the fixed atoms are connected to 
another group because of the bond connection. Hence, I just wonder whether I 
can connect the atoms from different groups like that.

You have said bonds between distinct molecules require a merged topology. Is 
there any introduction in the manual or Do you have any example about the 
merged topology?

Thank you for your reply .

Yang

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: Tuesday, April 21, 2009 5:49 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] about the bond connection between different groups

He, Yang wrote:
> Hi all users,
>
> I wonder whether it is allowed to define the bond connection between 
> different group in gromacs. Suppose atom A is in group1 and there is another 
> atom B in group2 .Then, I want to define bond between atom A and B. I am not 
> sure whether this is available in gromcas.
>

You'll have to elaborate on what you want to do.  Bonds are easily defined
within the topology.  Bonds between distinct molecules require a merged
topology, which is a bit more complicated.

-Justin

> Thank you for  any suggestions about that.
>
> Yang
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--


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


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[gmx-users] about the bond connection between different groups

[He, Yang]

Hi all users,

I wonder whether it is allowed to define the bond connection between different 
group in gromacs. Suppose atom A is in group1 and there is another atom B in 
group2 .Then, I want to define bond between atom A and B. I am not sure whether 
this is available in gromcas.

Thank you for  any suggestions about that.

Yang
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RE: [gmx-users] (no subject)

[He, Yang]

Hi Justin,

My version is a little old just 3.3.1 and I work in the LINUX system . As for 
my system, I have four single CG DNA model put in the box  randomly to see 
whether they can hybridize with the matched single strand while I need to keep 
the two strand fixed through fixing one or two atoms in that single strand .  
Hence, I use the position restraints to fix the two atoms in one single strand .

Yang





From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: Sunday, April 19, 2009 5:28 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] (no subject)

He, Yang wrote:
> Hi Justin,
>
> In fact, I have tried to use freezegrps to freeze a whole single CG DNA 
> strand  and it works but if I want to freeze some atoms in this single 
> strand, it seems that I have no choice but choose the position restraints. 
> The freezegrps seems not to work for that. But the error  for the position 
> restraints always is fragmentation fault and can not be fixed although many 
> methods have been tried.
>

So then the following is true:

freezegrps = DNA works fine
freezegrps = (your groups) gives "Invalid order for directive defaults"

That would make no sense.  The error comes from the topology, not anything
specified in the .mdp file, so I don't understand.

> I don't know whether this is a bug in the gromacs cause I have followed the 
> steps in manual to simulate a case(about speptide) in manual with position 
> restraints while it still doesn't work. I am confused about that.
>

I doubt it is a bug; this would be pretty prohibitory for most users.  It may be
specific to your system.  If you can provide details of your system, compilers,
which Gromacs version you are using (provided in a new thread that has a
noticeable subject line), you may be able to sort that issue out.

-Justin

> Yang
> 
> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
> Of Justin A. Lemkul [jalem...@vt.edu]
> Sent: Sunday, April 19, 2009 4:41 PM
> To: Gromacs Users' List
> Subject: Re: [gmx-users] (no subject)
>
> He, Yang wrote:
>> It always show the common error  "Invalid order for directive defaults".I 
>> suppose it is because I have  defined an atom belonging to two groups . What 
>> do you mean "by freezing subgroups of atoms
>> within a molecule" ? I just wonder how to make it ?Can you give me some 
>> examples?
>>
>
> The error is unrelated to your freezegrps.  See here:
>
> http://wiki.gromacs.org/index.php/Errors#Invalid_order_for_directive_defaults
>
> Your index groups should be fine.  A "subgroup" refers to select atoms within 
> a
> molecule, as in backbone of the protein, headgroups of lipids, or some such
> similar idea.  As I said before, your use of freezegrps and index groups 
> should,
> in theory, be fine.
>
> -Justin
>
>> Thank you very much.
>>
>> Yang
>> 
>> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On 
>> Behalf Of Justin A. Lemkul [jalem...@vt.edu]
>> Sent: Sunday, April 19, 2009 3:47 PM
>> To: Gromacs Users' List
>> Subject: Re: [gmx-users] (no subject)
>>
>> He, Yang wrote:
>>> Hi Justin,
>>>
>>> In fact, I just get the error. I have tried to use the freezegroup but it 
>>> seems that it only work for the whole group not certain atoms in the whole 
>>> group.
>>>
>> Alright, so what's the error?  You should be able to freeze subgroups of 
>> atoms
>> within a molecule; I've done it several times in different instances.
>>
>> -Justin
>>
>>> Yang
>>> 
>>> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On 
>>> Behalf Of Justin A. Lemkul [jalem...@vt.edu]
>>> Sent: Sunday, April 19, 2009 1:42 PM
>>> To: Discussion list for GROMACS users
>>> Subject: Re: [gmx-users] (no subject)
>>>
>>> He, Yang wrote:
>>>> Hi all users,
>>>>
>>>> I am trying to create the ndx file to define the atoms which I want to add 
>>>> the position restraints to. What I create is like this:
>>>>
>>>> [God]
>>>> 21  22
>>>> [Bad]
>>>> 61  62
>>>>
>>>> And  I have defined the atom numbering 21, 22, 61,62 in gro file like this 
>>>> :
>>>>
>>>> 2MOM   bT   21 0.805  1.330  3.914
>>>> 2MOM   bT  

RE: [gmx-users] (no subject)

[He, Yang]

Hi Justin,

In fact, I have tried to use freezegrps to freeze a whole single CG DNA strand  
and it works but if I want to freeze some atoms in this single strand, it seems 
that I have no choice but choose the position restraints. The freezegrps seems 
not to work for that. But the error  for the position restraints always is 
fragmentation fault and can not be fixed although many methods have been tried.

I don't know whether this is a bug in the gromacs cause I have followed the 
steps in manual to simulate a case(about speptide) in manual with position 
restraints while it still doesn't work. I am confused about that.

Yang

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: Sunday, April 19, 2009 4:41 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] (no subject)

He, Yang wrote:
> It always show the common error  "Invalid order for directive defaults".I 
> suppose it is because I have  defined an atom belonging to two groups . What 
> do you mean "by freezing subgroups of atoms
> within a molecule" ? I just wonder how to make it ?Can you give me some 
> examples?
>

The error is unrelated to your freezegrps.  See here:

http://wiki.gromacs.org/index.php/Errors#Invalid_order_for_directive_defaults

Your index groups should be fine.  A "subgroup" refers to select atoms within a
molecule, as in backbone of the protein, headgroups of lipids, or some such
similar idea.  As I said before, your use of freezegrps and index groups should,
in theory, be fine.

-Justin

> Thank you very much.
>
> Yang
> 
> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
> Of Justin A. Lemkul [jalem...@vt.edu]
> Sent: Sunday, April 19, 2009 3:47 PM
> To: Gromacs Users' List
> Subject: Re: [gmx-users] (no subject)
>
> He, Yang wrote:
>> Hi Justin,
>>
>> In fact, I just get the error. I have tried to use the freezegroup but it 
>> seems that it only work for the whole group not certain atoms in the whole 
>> group.
>>
>
> Alright, so what's the error?  You should be able to freeze subgroups of atoms
> within a molecule; I've done it several times in different instances.
>
> -Justin
>
>> Yang
>> 
>> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On 
>> Behalf Of Justin A. Lemkul [jalem...@vt.edu]
>> Sent: Sunday, April 19, 2009 1:42 PM
>> To: Discussion list for GROMACS users
>> Subject: Re: [gmx-users] (no subject)
>>
>> He, Yang wrote:
>>> Hi all users,
>>>
>>> I am trying to create the ndx file to define the atoms which I want to add 
>>> the position restraints to. What I create is like this:
>>>
>>> [God]
>>> 21  22
>>> [Bad]
>>> 61  62
>>>
>>> And  I have defined the atom numbering 21, 22, 61,62 in gro file like this :
>>>
>>> 2MOM   bT   21 0.805  1.330  3.914
>>> 2MOM   bT   22 0.448  1.572  3.576
>>>
>>>  4ICE   bT   61 0.805  4.330  3.914
>>>  4ICE   bT   62 0.448  4.572  3.576
>>>
>>> I know this may cause error cause I just define one atoms in two groups.   
>>> I just want to freeze only two atoms in the group[MOM](A single DNA strand) 
>>> while keep the other atoms in this group move freely , Meanwhile, the two 
>>> frozen atoms have a bond connection with the other atoms in this [MOM]group 
>>> ,which is assumed that this single DNA strand will be fixed because of the 
>>> two fixed atoms and the other atoms will move freely at the same time. I 
>>> wonder how I can define this position restraints in gromacs .
>>>
>> Are you assuming an error, or have you tried it and actually received an 
>> error?
>>   Use these groups as the "freezegrps" in the .mdp file and try it.  It 
>> should
>> be fine.
>>
>> -Justin
>>
>>> I hope what  I said is clear to you all and I really appreciate your any 
>>> suggestions.
>>>
>>> Yang
>>> ___
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/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.gromac

RE: [gmx-users] (no subject)

[He, Yang]

It always show the common error  "Invalid order for directive defaults".I 
suppose it is because I have  defined an atom belonging to two groups . What do 
you mean "by freezing subgroups of atoms
within a molecule" ? I just wonder how to make it ?Can you give me some 
examples?

Thank you very much.

Yang

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: Sunday, April 19, 2009 3:47 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] (no subject)

He, Yang wrote:
> Hi Justin,
>
> In fact, I just get the error. I have tried to use the freezegroup but it 
> seems that it only work for the whole group not certain atoms in the whole 
> group.
>

Alright, so what's the error?  You should be able to freeze subgroups of atoms
within a molecule; I've done it several times in different instances.

-Justin

> Yang
> 
> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
> Of Justin A. Lemkul [jalem...@vt.edu]
> Sent: Sunday, April 19, 2009 1:42 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] (no subject)
>
> He, Yang wrote:
>> Hi all users,
>>
>> I am trying to create the ndx file to define the atoms which I want to add 
>> the position restraints to. What I create is like this:
>>
>> [God]
>> 21  22
>> [Bad]
>> 61  62
>>
>> And  I have defined the atom numbering 21, 22, 61,62 in gro file like this :
>>
>> 2MOM   bT   21 0.805  1.330  3.914
>> 2MOM   bT   22 0.448  1.572  3.576
>>
>>  4ICE   bT   61 0.805  4.330  3.914
>>  4ICE   bT   62 0.448  4.572  3.576
>>
>> I know this may cause error cause I just define one atoms in two groups.   I 
>> just want to freeze only two atoms in the group[MOM](A single DNA strand) 
>> while keep the other atoms in this group move freely , Meanwhile, the two 
>> frozen atoms have a bond connection with the other atoms in this [MOM]group 
>> ,which is assumed that this single DNA strand will be fixed because of the 
>> two fixed atoms and the other atoms will move freely at the same time. I 
>> wonder how I can define this position restraints in gromacs .
>>
>
> Are you assuming an error, or have you tried it and actually received an 
> error?
>   Use these groups as the "freezegrps" in the .mdp file and try it.  It should
> be fine.
>
> -Justin
>
>> I hope what  I said is clear to you all and I really appreciate your any 
>> suggestions.
>>
>> Yang
>> ___
>> gmx-users mailing listgmx-users@gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
>>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
>

--


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


___
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RE: [gmx-users] (no subject)

[He, Yang]

Hi Justin,

In fact, I just get the error. I have tried to use the freezegroup but it seems 
that it only work for the whole group not certain atoms in the whole group.

Yang

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: Sunday, April 19, 2009 1:42 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] (no subject)

He, Yang wrote:
> Hi all users,
>
> I am trying to create the ndx file to define the atoms which I want to add 
> the position restraints to. What I create is like this:
>
> [God]
> 21  22
> [Bad]
> 61  62
>
> And  I have defined the atom numbering 21, 22, 61,62 in gro file like this :
>
> 2MOM   bT   21 0.805  1.330  3.914
> 2MOM   bT   22 0.448  1.572  3.576
>
>  4ICE   bT   61 0.805  4.330  3.914
>  4ICE   bT   62 0.448  4.572  3.576
>
> I know this may cause error cause I just define one atoms in two groups.   I 
> just want to freeze only two atoms in the group[MOM](A single DNA strand) 
> while keep the other atoms in this group move freely , Meanwhile, the two 
> frozen atoms have a bond connection with the other atoms in this [MOM]group 
> ,which is assumed that this single DNA strand will be fixed because of the 
> two fixed atoms and the other atoms will move freely at the same time. I 
> wonder how I can define this position restraints in gromacs .
>

Are you assuming an error, or have you tried it and actually received an error?
  Use these groups as the "freezegrps" in the .mdp file and try it.  It should
be fine.

-Justin

> I hope what  I said is clear to you all and I really appreciate your any 
> suggestions.
>
> Yang
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
>

--


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


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[gmx-users] (no subject)

[He, Yang]

Hi all users,

I am trying to create the ndx file to define the atoms which I want to add the 
position restraints to. What I create is like this:

[God]
21  22
[Bad]
61  62

And  I have defined the atom numbering 21, 22, 61,62 in gro file like this :

2MOM   bT   21 0.805  1.330  3.914
2MOM   bT   22 0.448  1.572  3.576

 4ICE   bT   61 0.805  4.330  3.914
 4ICE   bT   62 0.448  4.572  3.576

I know this may cause error cause I just define one atoms in two groups.   I 
just want to freeze only two atoms in the group[MOM](A single DNA strand) while 
keep the other atoms in this group move freely , Meanwhile, the two frozen 
atoms have a bond connection with the other atoms in this [MOM]group ,which is 
assumed that this single DNA strand will be fixed because of the two fixed 
atoms and the other atoms will move freely at the same time. I wonder how I can 
define this position restraints in gromacs .

I hope what  I said is clear to you all and I really appreciate your any 
suggestions.

Yang
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RE: [gmx-users] restrict two atoms in a group using freezegrps

[He, Yang]

HI Justin,

Thank you for your reply. I wonder what you mean by saying that I can specify a 
custom index group as your group
to be frozen. Can you give me a example about this ?

Thank you very much.

Yang

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: Saturday, April 18, 2009 11:59 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] restrict two atoms in a group using freezegrps

He, Yang wrote:
> HI all users,
>
> I have tried  a simple case with two atoms using [position_restraints] but 
> always it shows the same error :
>
> Segmentation fault (core dumped)
>
> But after I don't use the position_restraints for one atom and then I can run 
> the case smoothly. It seems that the gromacs doesn't recognize this 
> [position_restraints];
>

That may just indicate instability due to the restraints themselves; i.e.,
fixing atomic positions leads to a crash.

> Then, I tried the freezegrps but it seems to restrict a whole group. Here, I 
> wonder whether I can just use this method to restrict several atoms in a 
> whole group and how to do that.
>

Like any other Gromacs tool, you can specify a custom index group as your group
to be frozen.

-Justin

> Thank you for your any suggestions.
>
> Yang
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
>

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] restrict two atoms in a group using freezegrps

[He, Yang]

HI all users,

I have tried  a simple case with two atoms using [position_restraints] but 
always it shows the same error :

Segmentation fault (core dumped)

But after I don't use the position_restraints for one atom and then I can run 
the case smoothly. It seems that the gromacs doesn't recognize this 
[position_restraints];

Then, I tried the freezegrps but it seems to restrict a whole group. Here, I 
wonder whether I can just use this method to restrict several atoms in a whole 
group and how to do that.

Thank you for your any suggestions.

Yang
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[gmx-users] The way how to restrict atoms in gromacs

[He, Yang]

Hi all users,

I have used the position_restraints to restrict some atoms' activity but always 
it shows that Segmentation fault (core dumped).

I can not fix this problem after trying many methods and hence, I just wonder 
whether there are some other ways to restrict the atoms' movement in the 
gromacs.

Any suggestions will be highly appreciated .

Yang
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RE: [gmx-users] the position_restraints

[He, Yang]

Hi Justin,

I will list my mdp file  below:

integrator  = sd
dt  = 0.001
nsteps  = 20
comm_mode   = Linear; Linear, None, Angular
nstcomm = 0
comm-grps   = System
nstfout = 0
nstxout = 1000
nstvout = 1000
nstlog  = 1000nstenergy = 100
nstxtcout   = 100
xtc_grps= System
energygrps  = DNA
energygrp_excl  =
nstlist = 0
ns_type = simple
pbc = no; xyz, no (vacuum), full (infinite)
rlist   = 0
coulombtype = Cut-off
rcoulomb= 0
vdwtype = Cut-off
rvdw= 0
tcoupl  = no; for sd, tcoupl is ignored
tc-grps = System
tau_t   = 0.0347
ref_t   = 270
pcoupl  = no
gen_vel = yes
gen_temp= 300
gen_seed= 173529
constraints = none  ; none, all-bonds
freezegrps  =
freezedim   =

Thank you for your further suggestion.

Yang


From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: Tuesday, April 14, 2009 3:29 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] the position_restraints

He, Yang wrote:
> HI Justin,
>
> I just use the mdrun command and then get such error. Before that, I did not 
> get other messages just go on well expect when I use the mdrun.
>
> Also, when I did not use the position_restraints , it will run smoothly. As 
> long as I add this even though the position_restraints includes only one 
> atom, it will show the error.
>

This is difficult to diagnose exactly.  To me, removal of position restraints
suggests that you are fixing in place some bad contact that is causing your
system to crash.  Have a look at the trajectory to see what is going on.  Did EM
work properly?  If you are still having trouble, post a more complete
description of your system, relevant .mdp file(s), and anything else necessary
to try to get a resolution.

-Justin

> Yang
> 
> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
> Of Justin A. Lemkul [jalem...@vt.edu]
> Sent: Tuesday, April 14, 2009 3:06 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] the position_restraints
>
> He, Yang wrote:
>> HI all users,
>>
>> I want to define the position_restraints in the itp file but when I run it, 
>> it always show that
>>
>> Segmentation fault (core dumped)
>>
>
> You'll have to do better than "run it" - what do you mean, grompp? mdrun?
>
> As written, your position restraints look OK, so I don't think the problem is
> related to that section, necessarily.  How have you deduced that this is where
> the problem lies?
>
> Are you getting any other messages from (grompp? mdrun?) before the seg fault?
>
> -Justin
>
>> and I will list the part below:
>>
>>  [position_restraints]
>> ;ai funct fc
>>   111   1   1
>>   211   1   1
>>   311   1   1
>>   411   1   1
>>   511   1   1
>>   611   1   1
>>   711   1   1
>>   811   1   1
>>   911   1   1
>>  1011   1   1
>>  1111   1   1
>>  1211   1   1
>>  1311   1   1
>>  1411   1   1
>>  1511   1   1
>>  1611   1   1
>>  1711   1   1
>>  1811   1   1
>>  1911   1   1
>>  2011   1   1
>>  4111   1   1
>>  4211   1   1
>>  4311   1   1
>>  4411   1   1
>>  4511   1   1
>>  4611   1   1
>>  4711   1   1
>>  4811   1   1
>>  4911   1   1
>>  5011   1   1
>>  5111   1   1
>>  5211   1   1
>>  5311   1   1
>>  5411   1   1
>>  5511   1   1
>>  5611   1   1
>>  5711   1   10

RE: [gmx-users] the position_restraints

[He, Yang]

HI Justin,

I just use the mdrun command and then get such error. Before that, I did not 
get other messages just go on well expect when I use the mdrun.

Also, when I did not use the position_restraints , it will run smoothly. As 
long as I add this even though the position_restraints includes only one atom, 
it will show the error.

Yang

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: Tuesday, April 14, 2009 3:06 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] the position_restraints

He, Yang wrote:
> HI all users,
>
> I want to define the position_restraints in the itp file but when I run it, 
> it always show that
>
> Segmentation fault (core dumped)
>

You'll have to do better than "run it" - what do you mean, grompp? mdrun?

As written, your position restraints look OK, so I don't think the problem is
related to that section, necessarily.  How have you deduced that this is where
the problem lies?

Are you getting any other messages from (grompp? mdrun?) before the seg fault?

-Justin

> and I will list the part below:
>
>  [position_restraints]
> ;ai funct fc
>   111   1   1
>   211   1   1
>   311   1   1
>   411   1   1
>   511   1   1
>   611   1   1
>   711   1   1
>   811   1   1
>   911   1   1
>  1011   1   1
>  1111   1   1
>  1211   1   1
>  1311   1   1
>  1411   1   1
>  1511   1   1
>  1611   1   1
>  1711   1   1
>  1811   1   1
>  1911   1   1
>  2011   1   1
>  4111   1   1
>  4211   1   1
>  4311   1   1
>  4411   1   1
>  4511   1   1
>  4611   1   1
>  4711   1   1
>  4811   1   1
>  4911   1   1
>  5011   1   1
>  5111   1   1
>  5211   1   1
>  5311   1   1
>  5411   1   1
>  5511   1   1
>  5611   1   1
>  5711   1   1
>  5811   1   1
>  5911   1   1
>  6011   1   1
>
> Can anyone of you tell me what is the problem for that?  Thank you very much 
> in advance.
>
> Yang
> ___
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--


Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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] the position_restraints

[He, Yang]

HI all users,

I want to define the position_restraints in the itp file but when I run it, it 
always show that

Segmentation fault (core dumped)

and I will list the part below:

 [position_restraints]
;ai funct fc
  111   1   1
  211   1   1
  311   1   1
  411   1   1
  511   1   1
  611   1   1
  711   1   1
  811   1   1
  911   1   1
 1011   1   1
 1111   1   1
 1211   1   1
 1311   1   1
 1411   1   1
 1511   1   1
 1611   1   1
 1711   1   1
 1811   1   1
 1911   1   1
 2011   1   1
 4111   1   1
 4211   1   1
 4311   1   1
 4411   1   1
 4511   1   1
 4611   1   1
 4711   1   1
 4811   1   1
 4911   1   1
 5011   1   1
 5111   1   1
 5211   1   1
 5311   1   1
 5411   1   1
 5511   1   1
 5611   1   1
 5711   1   1
 5811   1   1
 5911   1   1
 6011   1   1

Can anyone of you tell me what is the problem for that?  Thank you very much in 
advance.

Yang
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[gmx-users] how to define the dummy atoms in gromacs

[He, Yang]

Hi all users,

I need to add some dummy atoms in my case. I know that I need to include the 
section [virtual_sites] in the top file but I am not sure how to define them in 
the itp file .Do I need to list these atoms in the section[atoms] ? Can anyone 
of you give me some suggestions about that?

Thank you in advance.

Yang
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[gmx-users] how to deal with the hydrogen bonding interactions between bases

[He, Yang]

Hi all users,

I need to define the hydrogen bonding interactions between bases in the CG DNA 
model . Can anyone of you tell me how to do that in the gromacs force files?

Thank you very much in advance.

Yang
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RE: [gmx-users] input the gro and trr file into the VMD

[He, Yang]

Hi,

I am sorry for that cause every time I sent my question, it shows that this 
email was not delivered and hence, I just tried for many times.

Yang


From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: Thursday, February 19, 2009 2:59 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] input the gro and trr file into the VMD

You've posted the same exact question five times today, even though you got a
very good response already:

http://www.gromacs.org/pipermail/gmx-users/2009-February/039830.html

If you want free advice, take what you're given, demonstrate that you've made
some efforts to solve your problem, and follow up if you experience a *new* 
issue.

-Justin

He, Yang wrote:
> Hi all users,
>
> When I try to input the .gro and .trr file into the VMD, I always find that 
> there is no bond connected among the atoms.But in fact, I have defined all 
> the bond connection in the gromacs files. Can anyone tell me how to get the 
> snap shots in the VMD with the bonds among the atoms?
>
> Thank you in advance.
>
> Yang
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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>

--


Justin A. Lemkul
Graduate Research Assistant
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] input the gro and trr file into the VMD

[He, Yang]

Hi all users,

When I try to input the .gro and .trr file into the VMD, I always find that 
there is no bond connected among the atoms.But in fact, I have defined all the 
bond connection in the gromacs files. Can anyone tell me how to get the snap 
shots in the VMD with the bonds among the atoms?

Thank you in advance.

Yang
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[gmx-users] (no subject)

[He, Yang]

Hi all users,

When I try to input the .gro and .trr file into the VMD, I always find that 
there is no bond connected among the atoms.But in fact, I have defined all the 
bond connection in the gromacs files. Can anyone tell me how to get the snap 
shots in the VMD with the bonds among the atoms?

Thank you in advance.

Yang
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[gmx-users] input the gro and trr file into the VMD

[He, Yang]

Hi all users,

When I try to input the .gro and .trr file into the VMD, I always find that 
there is no bond connected among the atoms.But in fact, I have defined all the 
bond connection in the gromacs files. Can anyone tell me how to get the snap 
shots in the VMD with the bonds among the atoms?

Thank you in advance.

Yang
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[gmx-users] trajectory file in the VMD

[He, Yang]

Hi all users,

When I try to input the .gro and .trr file into the VMD, I always find that 
there is no bond connected among the atoms.But in fact, I have defined all the 
bond connection in the gromacs files. Can anyone tell me how to get the snap 
shots in the VMD with the bonds among the atoms?

Thank you in advance.

Yang
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[gmx-users] input the gro and trr file into the VMD

[He, Yang]

Hi all users,

When I try to input the .gro and .trr file into the VMD, I always find that 
there is no bond connected among the atoms.But in fact, I have defined all the 
bond connection in the gromacs files. Can anyone tell me how to get the snap 
shots in the VMD with the bonds among the atoms?

Thank you in advance.

Yang
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RE: [gmx-users] about the repelling of DNA base pair

[He, Yang]

Hi, I just got this CG DNA model from a paper as well as the required 
parameters . What you think I should deal with the interactions about hydrogen 
bonding ? I have defined all the atoms' charge as 0 but still the repelling 
happened.

Yang

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: Thursday, February 05, 2009 3:58 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] about the repelling of DNA base pair

He, Yang wrote:
> Hi all users,
>
> I am dealing with  the CG DNA model and I just list the parameters for 
> non-bond potential blow:
>
>   A T 10.00690.04109
>
>   P P 10.04352   4.352E-12
>
>   S S 10.04352   4.352E-12
>
>   A A 10.02177   1.0894852E-12
>
>   T T 10.02177   1.0894852E-12
>   C G 10.00970.05422
>   C C 10.02177   1.0894852E-12
>   G G 10.02177   1.0894852E-12
>
>   A S 10.04352   4.352E-12
>
>   A P 10.04352   4.352E-12
>   A C 10.02177   1.0894852E-12
>   A G 10.02177   1.0894852E-12
>
>   T S 10.04352   4.352E-12
>
>   T P 10.04352   4.352E-12
>   T C 10.02177   1.0894852E-12
>   T G 10.02177   1.0894852E-12
>   C S 10.04352   4.352E-12
>   C P 10.04352   4.352E-12
>   G S 10.04352   4.352E-12
>   G P 10.04352   4.352E-12
>
>   S P 10.04352   4.352E-12
>
> You can see that the base pair potential is larger than the other pairs . But 
> I found when I run this case,using the command "ngmx",  it always shows that 
> the matching base pair will repel from each other even I set the temperature 
> by 0K in the mdp.file . I have checked the base pairs' distance and 
> originally they are all in the equilibrium distance.
>

Then your model physics are unrealistic.  Either the parameters are wrong, or
your .mdp options are inappropriate.  Do your nucleotides really just consist of
three particles (base, sugar, and phosphate)?  If so, you may be missing some of
the subtleties of hydrogen bonding (which is an electrostatic interaction), and
the geometry within the helix, and perhaps even causing excessive repulsion
between the phosphate backbones.

-Justin

> Thank you for any suggestions in advance.
>
> Yang
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>

--


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


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[gmx-users] about the repelling of DNA base pair

[He, Yang]

Hi all users,

I am dealing with  the CG DNA model and I just list the parameters for non-bond 
potential blow:

  A T 10.00690.04109

  P P 10.04352   4.352E-12

  S S 10.04352   4.352E-12

  A A 10.02177   1.0894852E-12

  T T 10.02177   1.0894852E-12
  C G 10.00970.05422
  C C 10.02177   1.0894852E-12
  G G 10.02177   1.0894852E-12

  A S 10.04352   4.352E-12

  A P 10.04352   4.352E-12
  A C 10.02177   1.0894852E-12
  A G 10.02177   1.0894852E-12

  T S 10.04352   4.352E-12

  T P 10.04352   4.352E-12
  T C 10.02177   1.0894852E-12
  T G 10.02177   1.0894852E-12
  C S 10.04352   4.352E-12
  C P 10.04352   4.352E-12
  G S 10.04352   4.352E-12
  G P 10.04352   4.352E-12

  S P 10.04352   4.352E-12

You can see that the base pair potential is larger than the other pairs . But I 
found when I run this case,using the command "ngmx",  it always shows that the 
matching base pair will repel from each other even I set the temperature by 0K 
in the mdp.file . I have checked the base pairs' distance and originally they 
are all in the equilibrium distance.

Thank you for any suggestions in advance.

Yang
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[gmx-users] how to get the original pdb file about CG DNA model

[He, Yang]

Hi all users,

I am wondering how to get the original pdb file for CG DNA model. I have looked 
for this file in the website but  no pdb file. Can anyone of you give me some 
suggestions how to get such file ?

Thank you in advance.

Yang
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RE: [gmx-users] the wanging: atom names don't match in top and gro file

[He, Yang]

Hi Mark,

You mean my format in the .GRO file is not very correct. What do you mean by 
saying " the second column one
too far to the right." ?

Thank you very much.

Yang

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
Of Mark Abraham [mark.abra...@anu.edu.au]
Sent: Tuesday, January 27, 2009 5:43 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] the wanging: atom names don't match in top and gro 
file

He, Yang wrote:
> Hi all users,
>
> when I run the command grompp , it always shows that
>
> processing coordinates...
> Warning: atom names in DNA.top and DNA.gro don't match (N10 - N1)
> Warning: atom names in DNA.top and DNA.gro don't match (Q11 - Q1)
> Warning: atom names in DNA.top and DNA.gro don't match (Q12 - Q1)
> Warning: atom names in DNA.top and DNA.gro don't match (C13 - C1)
> Warning: atom names in DNA.top and DNA.gro don't match (C14 - C1)
> Warning: atom names in DNA.top and DNA.gro don't match (N15 - N1)
> Warning: atom names in DNA.top and DNA.gro don't match (N16 - N1)
> Warning: atom names in DNA.top and DNA.gro don't match (Q17 - Q1)
> Warning: atom names in DNA.top and DNA.gro don't match (Q18 - Q1)
>  Warning: atom names in DNA.top and DNA.gro don't match (C19 - C1)
> Warning: atom names in DNA.top and DNA.gro don't match (C20 - C2)
>  Warning: atom names in DNA.top and DNA.gro don't match (N21 - N2)
> Warning: atom names in DNA.top and DNA.gro don't match (N22 - N2)
> Warning: atom names in DNA.top and DNA.gro don't match (W - W2)
> Warning: atom names in DNA.top and DNA.gro don't match (W - W2)
> Warning: atom names in DNA.top and DNA.gro don't match (W - W2)
> Warning: atom names in DNA.top and DNA.gro don't match (W - W2)
> WARNING 1 [file "DNA.top", line 12]:
>   17 non-matching atom names
>   atom names from DNA.top will be used
>   atom names from DNA.gro will be ignored
>
> I have checked that for some times but the warning is still on. I will list 
> the content below:
>  for .GRO FILE
> 1DNA N10  10   0.668430  0.387405  6.709000
> 1DNA Q11  11  -5.736999  6.827887  5.566000
> 1DNA Q12  12   8.266537 -3.346277  4.574000
> 1DNA C13  13  -1.947247  6.703736  4.66
> 1DNA C14  14   5.773899 -3.923511  2.10
> 1DNA N15  15   0.161888  0.755429  3.431000
> 1DNA N16  16   1.506403 -1.802878  3.189000
> 1DNA Q17  17  -0.627998  8.896000  2.186000
> 1DNA Q18  18   4.720877 -7.566143  1.194000
> 1DNA C19  19   2.365001  6.568000  1.28
> 1DNA C20  20   2.365001 -6.568000 -1.28
> 1DNA N21  21   0.159001  2.344000  0.191000
> 1DNA N22  22   0.575000 -0.516000 -0.051000

If the .gro format is fixed-format, then you have the second column one
too far to the right.

> FOR itp file
>
>   10Nda  1 DNA  N10   10   0
>   11Qa   1 DNA  Q11   11 -1.0
>   12Qa   1 DNA  Q12   12 -1.0
>   13C1 DNA  C13   13   0
>   14C1 DNA  C14   14   0
>   15Nda  1 DNA  N15   15   0
>   16Nda  1 DNA  N16   16   0
>   17Qa   1 DNA  Q17   17 -1.0
>   18Qa   1 DNA  Q18   18 -1.0
>   19C1 DNA  C19   19   0
>   20C1 DNA  C20   20   0
>   21Nda  1 DNA  N21   21   0
>   22Nda  1 DNA  N22   22   0
>
> Any suggestions will be appreciated .
>
> Regards,
>
> Yang
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[gmx-users] the wanging: atom names don't match in top and gro file

[He, Yang]

Hi all users,

when I run the command grompp , it always shows that

processing coordinates...
Warning: atom names in DNA.top and DNA.gro don't match (N10 - N1)
Warning: atom names in DNA.top and DNA.gro don't match (Q11 - Q1)
Warning: atom names in DNA.top and DNA.gro don't match (Q12 - Q1)
Warning: atom names in DNA.top and DNA.gro don't match (C13 - C1)
Warning: atom names in DNA.top and DNA.gro don't match (C14 - C1)
Warning: atom names in DNA.top and DNA.gro don't match (N15 - N1)
Warning: atom names in DNA.top and DNA.gro don't match (N16 - N1)
Warning: atom names in DNA.top and DNA.gro don't match (Q17 - Q1)
Warning: atom names in DNA.top and DNA.gro don't match (Q18 - Q1)
 Warning: atom names in DNA.top and DNA.gro don't match (C19 - C1)
Warning: atom names in DNA.top and DNA.gro don't match (C20 - C2)
 Warning: atom names in DNA.top and DNA.gro don't match (N21 - N2)
Warning: atom names in DNA.top and DNA.gro don't match (N22 - N2)
Warning: atom names in DNA.top and DNA.gro don't match (W - W2)
Warning: atom names in DNA.top and DNA.gro don't match (W - W2)
Warning: atom names in DNA.top and DNA.gro don't match (W - W2)
Warning: atom names in DNA.top and DNA.gro don't match (W - W2)
WARNING 1 [file "DNA.top", line 12]:
  17 non-matching atom names
  atom names from DNA.top will be used
  atom names from DNA.gro will be ignored

I have checked that for some times but the warning is still on. I will list the 
content below:
 for .GRO FILE
1DNA N10  10   0.668430  0.387405  6.709000
1DNA Q11  11  -5.736999  6.827887  5.566000
1DNA Q12  12   8.266537 -3.346277  4.574000
1DNA C13  13  -1.947247  6.703736  4.66
1DNA C14  14   5.773899 -3.923511  2.10
1DNA N15  15   0.161888  0.755429  3.431000
1DNA N16  16   1.506403 -1.802878  3.189000
1DNA Q17  17  -0.627998  8.896000  2.186000
1DNA Q18  18   4.720877 -7.566143  1.194000
1DNA C19  19   2.365001  6.568000  1.28
1DNA C20  20   2.365001 -6.568000 -1.28
1DNA N21  21   0.159001  2.344000  0.191000
1DNA N22  22   0.575000 -0.516000 -0.051000

FOR itp file

  10Nda  1 DNA  N10   10   0
  11Qa   1 DNA  Q11   11 -1.0
  12Qa   1 DNA  Q12   12 -1.0
  13C1 DNA  C13   13   0
  14C1 DNA  C14   14   0
  15Nda  1 DNA  N15   15   0
  16Nda  1 DNA  N16   16   0
  17Qa   1 DNA  Q17   17 -1.0
  18Qa   1 DNA  Q18   18 -1.0
  19C1 DNA  C19   19   0
  20C1 DNA  C20   20   0
  21Nda  1 DNA  N21   21   0
  22Nda  1 DNA  N22   22   0

Any suggestions will be appreciated .

Regards,

Yang
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RE: [gmx-users] why the trajectory file is not output

[He, Yang]

Hi Mark,

I just choose a small number of steps but it also does not work.it always shows 
that

starting mdrun 'MODEL CYLINDER'
1 steps,300.0 ps.

Segmentation fault (core dumped)

I am not very sure about that.

Thank you .

Yang

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
Of Mark Abraham [mark.abra...@anu.edu.au]
Sent: Friday, January 23, 2009 12:53 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] why the trajectory file is not output

He, Yang wrote:
> I just tried it several times and still can not get the trajectory file. I am 
> using the 3.3.1 not new version but I can get the xtc or trr file when 
> running the other cases .

It seems unlikely you were able to run a million-step integration
several times to completion. Choose a small number of steps, allow mdrun
to run to completion, and *then* see if your problem is real.

Mark
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RE: [gmx-users] why the trajectory file is not output

[He, Yang]

I just tried it several times and still can not get the trajectory file. I am 
using the 3.3.1 not new version but I can get the xtc or trr file when running 
the other cases .

Yang

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: Friday, January 23, 2009 12:09 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] why the trajectory file is not output

He, Yang wrote:
> yes, I mean that when using the command "mdrun", the traj.xtc file is not 
> ouput at all while the other files like "topol.tpr, ener.edr,md.log, 
> mdout.mdp" are all output.
>

Well, neither topol.tpr nor mdout.mdp are produced by mdrun (they are produced
by grompp), so that doesn't suggest anything important.

There are several questions that might provide some useful information:

1. Do md.log or ener.edr continue to get written to?
2. Is a .trr ever produced?  Its absence leads me to believe that you are simply
not being patient :)  As I said before, data is buffered and not continually 
output.
3. What version of Gromacs are you using?  Are you running in parallel, and if
so, do other MPI codes work on the same box/cluster?

-Justin

> Hence, I just got confused about that.
>
> Yang
> 
> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
> Of Justin A. Lemkul [jalem...@vt.edu]
> Sent: Friday, January 23, 2009 11:55 AM
> To: Gromacs Users' List
> Subject: Re: [gmx-users] why the trajectory file is not output
>
> He, Yang wrote:
>> I think this problem is  not due to the disk space cause I check that it has 
>> a large space in the fold. I have tried some times but always the same 
>> results  ,no trajectory files while the others are normal .
>>
>
> What files are produced?  And again, are you referring to the absence of the
> trajectory *during* the simulation, or after?  Which trajectory, .trr or .xtc,
> is missing?
>
> -Justin
>
>> Thank you very much for your reply.
>>
>> Yang
>> 
>> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On 
>> Behalf Of Justin A. Lemkul [jalem...@vt.edu]
>> Sent: Friday, January 23, 2009 11:42 AM
>> To: Discussion list for GROMACS users
>> Subject: Re: [gmx-users] why the trajectory file is not output
>>
>> He, Yang wrote:
>>> Hi all the users,
>>>
>>> When I use the command "mdrun"to simulate the CG DNA model, I found that  
>>> all the  files are output expect the trajectory file. I will list some 
>>> parts of my mdp.file
>>>
>> During the simulation?  Data is buffered, so you may not see immediate 
>> output.
>> Or is the trajectory absent at the end of the simulation?  That might 
>> indicate a
>>   problem with available disk space, depending on how large the file is.
>>
>> -Justin
>>
>>> ; RUN CONTROL PARAMETERS =
>>> integrator   = md
>>> ; start time and timestep in ps =
>>> tinit= 0.0
>>> dt   = 0.03
>>> nsteps   = 100
>>> ; number of steps for center of mass motion removal =
>>> nstcomm  = 1
>>>
>>>
>>> ; OUTPUT CONTROL OPTIONS =
>>> ; Output frequency for coords (x), velocities (v) and forces (f) =
>>> nstxout  = 5000
>>> nstvout  = 5000
>>> nstfout  = 0
>>> ; Output frequency for energies to log file and energy file =
>>> nstlog   = 1000
>>> nstenergy= 1000
>>> ; Output frequency and precision for xtc file =
>>> nstxtcout= 1000
>>> xtc_precision= 1000
>>> ; This selects the subset of atoms for the xtc file. You can =
>>> ; select multiple groups. By default all atoms will be written. =
>>> xtc-grps =
>>> ; Selection of energy groups =
>>> energygrps   = plan1 NA CL W
>>>
>>> ; NEIGHBORSEARCHING PARAMETERS =
>>> ; nblist update frequency =
>>> nstlist  = 10
>>> ; ns algorithm (simple or grid) =
>>> ns_type  = grid
>>> ; Periodic boundary conditions: xyz or none =
>>> pbc  = xyz
>>> ; nblist cut-off =
>>> rlist= 1.2
>>> domain-decomposition = no
>>>
>>> ; OPTIONS FOR ELECTROSTATICS AND VDW =
>>> ; M

RE: [gmx-users] why the trajectory file is not output

[He, Yang]

yes, I mean that when using the command "mdrun", the traj.xtc file is not ouput 
at all while the other files like "topol.tpr, ener.edr,md.log, mdout.mdp" are 
all output.

Hence, I just got confused about that.

Yang

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: Friday, January 23, 2009 11:55 AM
To: Gromacs Users' List
Subject: Re: [gmx-users] why the trajectory file is not output

He, Yang wrote:
> I think this problem is  not due to the disk space cause I check that it has 
> a large space in the fold. I have tried some times but always the same 
> results  ,no trajectory files while the others are normal .
>

What files are produced?  And again, are you referring to the absence of the
trajectory *during* the simulation, or after?  Which trajectory, .trr or .xtc,
is missing?

-Justin

> Thank you very much for your reply.
>
> Yang
> 
> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
> Of Justin A. Lemkul [jalem...@vt.edu]
> Sent: Friday, January 23, 2009 11:42 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] why the trajectory file is not output
>
> He, Yang wrote:
>> Hi all the users,
>>
>> When I use the command "mdrun"to simulate the CG DNA model, I found that  
>> all the  files are output expect the trajectory file. I will list some parts 
>> of my mdp.file
>>
>
> During the simulation?  Data is buffered, so you may not see immediate output.
> Or is the trajectory absent at the end of the simulation?  That might 
> indicate a
>   problem with available disk space, depending on how large the file is.
>
> -Justin
>
>> ; RUN CONTROL PARAMETERS =
>> integrator   = md
>> ; start time and timestep in ps =
>> tinit= 0.0
>> dt   = 0.03
>> nsteps   = 100
>> ; number of steps for center of mass motion removal =
>> nstcomm  = 1
>>
>>
>> ; OUTPUT CONTROL OPTIONS =
>> ; Output frequency for coords (x), velocities (v) and forces (f) =
>> nstxout  = 5000
>> nstvout  = 5000
>> nstfout  = 0
>> ; Output frequency for energies to log file and energy file =
>> nstlog   = 1000
>> nstenergy= 1000
>> ; Output frequency and precision for xtc file =
>> nstxtcout= 1000
>> xtc_precision= 1000
>> ; This selects the subset of atoms for the xtc file. You can =
>> ; select multiple groups. By default all atoms will be written. =
>> xtc-grps =
>> ; Selection of energy groups =
>> energygrps   = plan1 NA CL W
>>
>> ; NEIGHBORSEARCHING PARAMETERS =
>> ; nblist update frequency =
>> nstlist  = 10
>> ; ns algorithm (simple or grid) =
>> ns_type  = grid
>> ; Periodic boundary conditions: xyz or none =
>> pbc  = xyz
>> ; nblist cut-off =
>> rlist= 1.2
>> domain-decomposition = no
>>
>> ; OPTIONS FOR ELECTROSTATICS AND VDW =
>> ; Method for doing electrostatics =
>> coulombtype  = PME
>> rcoulomb_switch  = 0.0
>> rcoulomb = 1.2
>> ; Dielectric constant (DC) for cut-off or DC of reaction field =
>> epsilon_r= 20
>> ; Method for doing Van der Waals =
>> vdw_type = Shift
>> ; cut-off lengths=
>> rvdw_switch  = 0.9
>> rvdw = 1.15
>> ; Apply long range dispersion corrections for Energy and Pressure =
>> DispCorr = No
>> ; Spacing for the PME/PPPM FFT grid =
>> fourierspacing   = 0.3
>> ; FFT grid size, when a value is 0 fourierspacing will be used =
>> fourier_nx   = 0
>> fourier_ny   = 0
>> fourier_nz   = 0
>> ; EWALD/PME/PPPM parameters =
>> pme_order= 4
>> ewald_rtol   = 1e-05
>> epsilon_surface  = 0
>> optimize_fft = yes
>>
>> ; OPTIONS FOR WEAK COUPLING ALGORITHMS =
>> ; Temperature coupling   =
>> tcoupl   = Berendsen
>> ; Groups to couple separately =
>> tc-grps  = plan1 NA CL W
>> ; Time constant (ps) and reference temperature (K) =
>> tau_t= 1.0 1.0 1.0 1.0
>> ref_t= 300 300

RE: [gmx-users] why the trajectory file is not output

[He, Yang]

I think this problem is  not due to the disk space cause I check that it has a 
large space in the fold. I have tried some times but always the same results  
,no trajectory files while the others are normal .

Thank you very much for your reply.

Yang

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: Friday, January 23, 2009 11:42 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] why the trajectory file is not output

He, Yang wrote:
> Hi all the users,
>
> When I use the command "mdrun"to simulate the CG DNA model, I found that  all 
> the  files are output expect the trajectory file. I will list some parts of 
> my mdp.file
>

During the simulation?  Data is buffered, so you may not see immediate output.
Or is the trajectory absent at the end of the simulation?  That might indicate a
  problem with available disk space, depending on how large the file is.

-Justin

> ; RUN CONTROL PARAMETERS =
> integrator   = md
> ; start time and timestep in ps =
> tinit= 0.0
> dt   = 0.03
> nsteps   = 100
> ; number of steps for center of mass motion removal =
> nstcomm  = 1
>
>
> ; OUTPUT CONTROL OPTIONS =
> ; Output frequency for coords (x), velocities (v) and forces (f) =
> nstxout  = 5000
> nstvout  = 5000
> nstfout  = 0
> ; Output frequency for energies to log file and energy file =
> nstlog   = 1000
> nstenergy= 1000
> ; Output frequency and precision for xtc file =
> nstxtcout= 1000
> xtc_precision= 1000
> ; This selects the subset of atoms for the xtc file. You can =
> ; select multiple groups. By default all atoms will be written. =
> xtc-grps =
> ; Selection of energy groups =
> energygrps   = plan1 NA CL W
>
> ; NEIGHBORSEARCHING PARAMETERS =
> ; nblist update frequency =
> nstlist  = 10
> ; ns algorithm (simple or grid) =
> ns_type  = grid
> ; Periodic boundary conditions: xyz or none =
> pbc  = xyz
> ; nblist cut-off =
> rlist= 1.2
> domain-decomposition = no
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW =
> ; Method for doing electrostatics =
> coulombtype  = PME
> rcoulomb_switch  = 0.0
> rcoulomb = 1.2
> ; Dielectric constant (DC) for cut-off or DC of reaction field =
> epsilon_r= 20
> ; Method for doing Van der Waals =
> vdw_type = Shift
> ; cut-off lengths=
> rvdw_switch  = 0.9
> rvdw = 1.15
> ; Apply long range dispersion corrections for Energy and Pressure =
> DispCorr = No
> ; Spacing for the PME/PPPM FFT grid =
> fourierspacing   = 0.3
> ; FFT grid size, when a value is 0 fourierspacing will be used =
> fourier_nx   = 0
> fourier_ny   = 0
> fourier_nz   = 0
> ; EWALD/PME/PPPM parameters =
> pme_order= 4
> ewald_rtol   = 1e-05
> epsilon_surface  = 0
> optimize_fft = yes
>
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS =
> ; Temperature coupling   =
> tcoupl   = Berendsen
> ; Groups to couple separately =
> tc-grps  = plan1 NA CL W
> ; Time constant (ps) and reference temperature (K) =
> tau_t= 1.0 1.0 1.0 1.0
> ref_t= 300 300 300 300
> ; Pressure coupling  =
> Pcoupl   = no
> Pcoupltype   = Isotropic
> ; Time constant (ps), compressibility (1/bar) and reference P (bar) =
> tau_p= 1.0
> compressibility  = 1e-5
> ref_p= 1.0
>
>
> ; SIMULATED ANNEALING CONTROL =
> annealing= no
> ; Time at which temperature should be zero (ps) =
> zero_temp_time   = 0
>
> ; GENERATE VELOCITIES FOR STARTUP RUN =
> gen_vel  = yes
> gen_temp = 300
> gen_seed = 473529
>
> ; OPTIONS FOR BONDS =
> constraints  = none
> ; Type of constraint algorithm =
> constraint_algorithm = Lincs
> ; Do not constrain the start configuration =
> unconstrained_start  = no
> ; Relative tolerance of shake =
> shake_tol= 0.0001
> ; Highest order in the expansion of the constraint coupling matrix =
> lincs_order  = 4
> ; Lincs will write a warning to the stderr if in one step a bond =
> ; rot

[gmx-users] why the trajectory file is not output

[He, Yang]

Hi all the users,

When I use the command "mdrun"to simulate the CG DNA model, I found that  all 
the  files are output expect the trajectory file. I will list some parts of my 
mdp.file

; RUN CONTROL PARAMETERS =
integrator   = md
; start time and timestep in ps =
tinit= 0.0
dt   = 0.03
nsteps   = 100
; number of steps for center of mass motion removal =
nstcomm  = 1


; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout  = 5000
nstvout  = 5000
nstfout  = 0
; Output frequency for energies to log file and energy file =
nstlog   = 1000
nstenergy= 1000
; Output frequency and precision for xtc file =
nstxtcout= 1000
xtc_precision= 1000
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
xtc-grps =
; Selection of energy groups =
energygrps   = plan1 NA CL W

; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist  = 10
; ns algorithm (simple or grid) =
ns_type  = grid
; Periodic boundary conditions: xyz or none =
pbc  = xyz
; nblist cut-off =
rlist= 1.2
domain-decomposition = no

; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype  = PME
rcoulomb_switch  = 0.0
rcoulomb = 1.2
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r= 20
; Method for doing Van der Waals =
vdw_type = Shift
; cut-off lengths=
rvdw_switch  = 0.9
rvdw = 1.15
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = No
; Spacing for the PME/PPPM FFT grid =
fourierspacing   = 0.3
; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
; EWALD/PME/PPPM parameters =
pme_order= 4
ewald_rtol   = 1e-05
epsilon_surface  = 0
optimize_fft = yes

; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling   =
tcoupl   = Berendsen
; Groups to couple separately =
tc-grps  = plan1 NA CL W
; Time constant (ps) and reference temperature (K) =
tau_t= 1.0 1.0 1.0 1.0
ref_t= 300 300 300 300
; Pressure coupling  =
Pcoupl   = no
Pcoupltype   = Isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p= 1.0
compressibility  = 1e-5
ref_p= 1.0


; SIMULATED ANNEALING CONTROL =
annealing= no
; Time at which temperature should be zero (ps) =
zero_temp_time   = 0

; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel  = yes
gen_temp = 300
gen_seed = 473529

; OPTIONS FOR BONDS =
constraints  = none
; Type of constraint algorithm =
constraint_algorithm = Lincs
; Do not constrain the start configuration =
unconstrained_start  = no
; Relative tolerance of shake =
shake_tol= 0.0001
; Highest order in the expansion of the constraint coupling matrix =
lincs_order  = 4
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs_warnangle  = 30
; Convert harmonic bonds to morse potentials =
morse= no

; NMR refinement stuff  =
; Distance restraints type: No, Simple or Ensemble =
disre= No
; Force weighting of pairs in one distance restraint: Equal or Conservative =
disre_weighting  = Equal
; Use sqrt of the time averaged times the instantaneous violation =
disre_mixed  = no
disre_fc = 1000
disre_tau= 1.25
; Output frequency for pair distances to energy file =
nstdisreout  = 100

; Free energy control stuff =
free_energy  = no
init_lambda  = 0
delta_lambda = 0
sc-alpha = 0
sc-sigma = 0.3

; Non-equilibrium MD stuff =
acc-grps =
accelerate   =
freezegrps   =
freezedim=
cos-acceleration =
energygrp_excl   =

; Electric fields   =
; Format is number of terms (int) and for all terms an amplitude (real) =
; and a phase angle (real) =
E-x  =
E-xt =
E-y  = 1 0.05 0.0
E-yt =
E-z  =
E-zt =

; User defined thingies =
user1-grps   =
user2-grps   =
userint1   

RE: [gmx-users] course grain model for DNA

[He, Yang]

Hi Mrinalini.

Thank you for your suggestions. In my previous case, I never use the distance 
restraints . So I wonder whether you can provide me a sample for file of the 
disres.itp .In fact, I don't know much about this file' form and how to set 
values in the file.

Thank you.

Yang

From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Mrinalini Puranik [EMAIL 
PROTECTED]
Sent: Tuesday, November 25, 2008 3:59 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] course grain model for DNA

If there is fraying at the edges only, you can impose distance
restraints on some of the hydrogen bonds at the ends. You need to
modify md.mdp to turn on distance restraints and have a new file
called disres.itp that mentions the distances to be restrained.

Hope this helps,
Mrinalini


On Wed, Nov 26, 2008 at 1:06 AM, He, Yang <[EMAIL PROTECTED]> wrote:
> Hi all users,
>
> when I am using the gromacs to simulate the course grain model for DNA, it 
> seems that the software doesn't recognize my force field file. I have 
> included all the bond and non-bond parameters in the bon.itp and nb.itp file.
>
> During my simulation , I found that the base pair for C-G which first are in 
> the balance distance always repel from each other so I try to increase the 
> value of epsilon to increase the dispersion between this pair but it still 
> did not work and the pair still  repelled  from each other after the 
> simulation .
>
> Then I tried like this "   ;  Gb2  Cb2  1  0.000194e10   0.00217e4 " 
> in my nb.itp file,  I found that the simulation can still be carried on and 
> the simulation result is the same for this base pair.
>
> So ,I got confused about this phenomenon . Can anyone of you give me some 
> suggestions?
>
> Thank you in advance.
>
> Yang
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to [EMAIL PROTECTED]
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>



--
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RE: [gmx-users] course grain model for DNA

[He, Yang]

Hi Justin,

Thank you for your reply. In fact , for this base pair of "Gb2  Cb2  1  
0.000194e10   0.00217e4",  whatever I do , the final result for this base pair 
is the same they will always separate from each other. Hence, I doubt whether 
this is because gromacs did not read my force field file at all.

I hope to get your further suggestions about that.

Thank you .

Yang

From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Justin A. Lemkul [EMAIL 
PROTECTED]
Sent: Tuesday, November 25, 2008 3:06 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] course grain model for DNA

He, Yang wrote:
> Hi all users,
>
> when I am using the gromacs to simulate the course grain model for DNA, it 
> seems that the software doesn't recognize my force field file. I have 
> included all the bond and non-bond parameters in the bon.itp and nb.itp file.
>
> During my simulation , I found that the base pair for C-G which first are in 
> the balance distance always repel from each other so I try to increase the 
> value of epsilon to increase the dispersion between this pair but it still 
> did not work and the pair still  repelled  from each other after the 
> simulation .
>
> Then I tried like this "   ;  Gb2  Cb2  1  0.000194e10   0.00217e4 " 
> in my nb.itp file,  I found that the simulation can still be carried on and 
> the simulation result is the same for this base pair.
>

Well, that line is commented out (;), so naturally it would have no effect.

-Justin

> So ,I got confused about this phenomenon . Can anyone of you give me some 
> suggestions?
>
> Thank you in advance.
>
> Yang
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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> www interface or send it to [EMAIL PROTECTED]
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>

--


Justin A. Lemkul
Graduate Research Assistant
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] course grain model for DNA

[He, Yang]

Hi all users,

when I am using the gromacs to simulate the course grain model for DNA, it 
seems that the software doesn't recognize my force field file. I have included 
all the bond and non-bond parameters in the bon.itp and nb.itp file.

During my simulation , I found that the base pair for C-G which first are in 
the balance distance always repel from each other so I try to increase the 
value of epsilon to increase the dispersion between this pair but it still did 
not work and the pair still  repelled  from each other after the simulation .

Then I tried like this "   ;  Gb2  Cb2  1  0.000194e10   0.00217e4 " in 
my nb.itp file,  I found that the simulation can still be carried on and the 
simulation result is the same for this base pair.

So ,I got confused about this phenomenon . Can anyone of you give me some 
suggestions?

Thank you in advance.

Yang
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[gmx-users] course grain model for DNA

[He, Yang]

Hi all users,

I just use the gromacs to simulate the course grain model for DNA, but   when I 
run the simulation to see whether the two strands will separate under certain 
temperature , I found that the disassociation will happen in the low 
temperature . This is my part of mdp.file

;VARIOUS PREPROCESSING OPTIONS
title= atom
; Preprocessor - specify a full path if necessary.
cpp  = cpp
define   =

; RUN CONTROL PARAMETERS
integrator   = md
; Start time and timestep in ps
tinit= 0
dt   = 0.002
nsteps   =10
; For exact run continuation or redoing part of a run
init_step= 0
; mode for center of mass motion removal
comm-mode= Linear
; number of steps for center of mass motion removal
nstcomm  = 1
; group(s) for center of mass motion removal
comm-grps=




; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist  = 10
; ns algorithm (simple or grid)
ns_type  = grid
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc  = xyz
; nblist cut-off
rlist= 0.686
domain-decomposition = no

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = Cutoff
rcoulomb-switch  = 0
rcoulomb = 0.9
; Relative dielectric constant for the Cut-off or DC of the reaction field
epsilon-r= 78
; Method for doing Van der Waals
vdw-type = Cutoff
; cut-off lengths
rvdw-switch  = 0
rvdw = 0.9
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension  = 1.0
; Seperate tables between energy group pairs
energygrp_table  =
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
; EWALD/PME/PPPM parameters
pme_order= 4
ewald_rtol   = 1e-05
ewald_geometry   = 3d
epsilon_surface  = 0
optimize_fft = no

; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm = Still
; Frequency of calculating the Born radii inside rlist
nstgbradii   = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii = 2
; Salt concentration in M for Generalized Born models
gb_saltconc  = 0

; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)
implicit_solvent = No


; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl   = berendsen
; Groups to couple separately
tc-grps  = System
; Time constant (ps) and reference temperature (K)
tau_t= 0.1
ref_t= 200
; Pressure coupling
Pcoupl   = no
Pcoupltype   = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p= 0.5
compressibility  = 4.5e-5
ref_p= 1.0
; Random seed for Andersen thermostat
andersen_seed= 815131


Can anyone who has the experience of dealing withe course grain model for DNA  
give me some suggestions about this phenomenon.

Any possible help will be highly appreciated .

Thank you very much.

Yang
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RE: [gmx-users] the temperature effect in the simulation

[He, Yang]

Hi Yuguang,

when I use the command ngmx to show the trajectory , I just choose the DNA 
group not including the water.

Any suggestions ? Thank you very much.

Yang

From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Mu Yuguang (Dr) [EMAIL 
PROTECTED]
Sent: Tuesday, November 11, 2008 12:17 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] the temperature effect in the simulation

Do you have water ?

-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Nicolas Sapay
Sent: 2008年11月12日 4:15
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] the temperature effect in the simulation

He, Yang wrote:
> Hi all users,
>
> When I change the temperature to try to get different disassociation about 
> the two DNA's strands. But even I change the value of temperature by 0K in 
> the mdp file ,
>
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> ; Temperature coupling
> Tcoupl   = berendsen
> ; Groups to couple separately
> tc-grps  = System
> ; Time constant (ps) and reference temperature (K)
> tau_t= 0.001
>
The coupling constant sounds a bit small. The dynamics of fast motions
may be affected more than you want, but I'm not a specialist of DNA and
I don't know if it's a problem in that particular case.
> ref_t= 300
>
This indicates that your target temperature is 300K not 0K
> ; Pressure coupling
> Pcoupl   = no
> Pcoupltype   = isotropic
> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
> tau_p= 0.5
> compressibility  = 4.5e-5
> ref_p= 1.0
> ; Random seed for Andersen thermostat
> andersen_seed= 815131
>
> It  will also disassociate .It is strange.
>
> Can anyone of you tell me what is the reason for that?
>
> Thank you in advance.
>
> Yang
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
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>
>

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RE: [gmx-users] the temperature effect in the simulation

[He, Yang]

Hi Justin,

My box size is 3.13690   3.73000   2.7 and I  use  the user-defined 
potential functions.

#define _FF_GROMACS
#define _FF_GROMACS1

[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
  1 1   no  1.0   1.0

#include "ffyxhnb.itp"
#include "ffyxhbon.itp"

This is my ffyxh.itp file

Also  I have change the value of  tau_t by 0.1 but it did not work.

Please let me know if you need any further information.

Thank you.

Yang

From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Justin A. Lemkul [EMAIL 
PROTECTED]
Sent: Tuesday, November 11, 2008 12:12 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] the temperature effect in the simulation

He, Yang wrote:
> Hi all users,
>
> When I change the temperature to try to get different disassociation about 
> the two DNA's strands. But even I change the value of temperature by 0K in 
> the mdp file ,
>
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> ; Temperature coupling
> Tcoupl   = berendsen
> ; Groups to couple separately
> tc-grps  = System
> ; Time constant (ps) and reference temperature (K)
> tau_t= 0.001
> ref_t= 300

I don't know if this is relevant or not, but a coupling constant of 0.001 is
exceptionally short.  What is the timestep in your simulation?  Typically one
sees tau_t = 0.1 with a timestep of 0.001-0.002 ps.

> ; Pressure coupling
> Pcoupl   = no
> Pcoupltype   = isotropic
> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
> tau_p= 0.5
> compressibility  = 4.5e-5
> ref_p= 1.0
> ; Random seed for Andersen thermostat
> andersen_seed= 815131
>
> It  will also disassociate .It is strange.

So the dissociation occurs at 0K and 300K?  Sounds like something is
fundamentally flawed with your system setup.  How large is your box?  What force
field are you using?

-Justin

>
> Can anyone of you tell me what is the reason for that?
>
> Thank you in advance.
>
> Yang
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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>

--


Justin A. Lemkul
Graduate Research Assistant
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] the temperature effect in the simulation

[He, Yang]

Hi all users,

When I change the temperature to try to get different disassociation about the 
two DNA's strands. But even I change the value of temperature by 0K in the mdp 
file ,

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl   = berendsen
; Groups to couple separately
tc-grps  = System
; Time constant (ps) and reference temperature (K)
tau_t= 0.001
ref_t= 300
; Pressure coupling
Pcoupl   = no
Pcoupltype   = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p= 0.5
compressibility  = 4.5e-5
ref_p= 1.0
; Random seed for Andersen thermostat
andersen_seed= 815131

It  will also disassociate .It is strange.

Can anyone of you tell me what is the reason for that?

Thank you in advance.

Yang
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RE: [gmx-users] the Temperature in the mdp.file

[He, Yang]

Hi Yang Ye,

Thank you for your reply. When I change the temperature, the disassociation 
about the two strands of DNA always happened even though the temperature is 
reduced to 0K. It is absolutely impossible.

I think it is a real disassociation. So I am confused about the phenomenon .

Any further suggestions ? I really appreciate your help.

Yang

From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Yang Ye [EMAIL PROTECTED]
Sent: Monday, November 10, 2008 6:35 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] the Temperature in the mdp.file

Is it a real diassociation or an illusion? Visualize with PBC in mind.
To put them back, use trjconv  to center one chain of the DNA and
output the two chains.

On 11/11/08, He, Yang <[EMAIL PROTECTED]> wrote:
Hi all users.
>
> When I change the Temperature in the madp file to try to get different result 
> about DNA model\'s disassociation , but it is strange that result seems to be 
> the same for different Temperature. Even I change the Temperature by 0K ,the 
> disassociation happened.
>
> I have tried to reduce the force between some bond and non-bond, but the 
> effect is not very good.
>
> This is part of my mdp file:
>
> ; RUN CONTROL PARAMETERS
> integrator   = md
> ; Start time and timestep in ps
> tinit= 0
> dt   = 0.0001
> nsteps   =10
> ; For exact run continuation or redoing part of a run
> init_step= 0
> ; mode for center of mass motion removal
> comm-mode= Linear
> ; number of steps for center of mass motion removal
> nstcomm  = 1
> ; group(s) for center of mass motion removal
> comm-grps=
>
>
>
>
> ; NEIGHBORSEARCHING PARAMETERS
> ; nblist update frequency
> nstlist  = 10
> ; ns algorithm (simple or grid)
> ns_type  = grid
> ; Periodic boundary conditions: xyz (default), no (vacuum)
> ; or full (infinite systems only)
> pbc  = xyz
> ; nblist cut-off
> rlist= 0.686
> domain-decomposition = no
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> ; Method for doing electrostatics
> coulombtype  = User
> rcoulomb-switch  = 0
> rcoulomb = 0.9
> ; Relative dielectric constant for the Cut-off or DC of the reaction field
> epsilon-r= 78
> ; Method for doing Van der Waals
> vdw-type = User
> ; cut-off lengths
> rvdw-switch  = 0
> rvdw = 0.9
> ; Apply long range dispersion corrections for Energy and Pressure
> DispCorr = EnerPres
> ; Extension of the potential lookup tables beyond the cut-off
> table-extension  = 1
> ; Seperate tables between energy group pairs
> energygrp_table  =
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing   = 0.12
> ; FFT grid size, when a value is 0 fourierspacing will be used
> fourier_nx   = 0
> fourier_ny   = 0
> fourier_nz   = 0
> ; EWALD/PME/PPPM parameters
> pme_order= 4
> ewald_rtol   = 1e-05
> ewald_geometry   = 3d
> epsilon_surface  = 0
> optimize_fft = no
>
> ; GENERALIZED BORN ELECTROSTATICS
> ; Algorithm for calculating Born radii
> gb_algorithm = Still
> ; Frequency of calculating the Born radii inside rlist
> nstgbradii   = 1
> ; Cutoff for Born radii calculation; the contribution from atoms
> ; between rlist and rgbradii is updated every nstlist steps
> rgbradii = 2
> ; Salt concentration in M for Generalized Born models
> gb_saltconc  = 0
>
> ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)
> implicit_solvent = No
>
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> ; Temperature coupling
> Tcoupl   = berendsen
> ; Groups to couple separately
> tc-grps  = System
> ; Time constant (ps) and reference temperature (K)
> tau_t= 0.1
> ref_t= 300
> ; Pressure coupling
> Pcoupl   = no
> Pcoupltype   = isotropic
> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
> tau_p= 0.5
> compressibility  = 4.5e-5
> ref_p= 1.0
> ; Random seed for Andersen thermostat
> andersen_seed= 815131
>
>
> Can anyone of you tell me what is the reason for that?
>
> Thank you in advance.
>
> Yang
>
> ___
> gmx-users mailing li

[gmx-users] the Temperature in the mdp.file

[He, Yang]

Hi all users.

When I change the Temperature in the madp file to try to get different result 
about DNA model's disassociation , but it is strange that result seems to be 
the same for different Temperature. Even I change the Temperature by 0K ,the 
disassociation happened.

I have tried to reduce the force between some bond and non-bond, but the effect 
is not very good.

This is part of my mdp file:

; RUN CONTROL PARAMETERS
integrator   = md
; Start time and timestep in ps
tinit= 0
dt   = 0.0001
nsteps   =10
; For exact run continuation or redoing part of a run
init_step= 0
; mode for center of mass motion removal
comm-mode= Linear
; number of steps for center of mass motion removal
nstcomm  = 1
; group(s) for center of mass motion removal
comm-grps=




; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist  = 10
; ns algorithm (simple or grid)
ns_type  = grid
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc  = xyz
; nblist cut-off
rlist= 0.686
domain-decomposition = no

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = User
rcoulomb-switch  = 0
rcoulomb = 0.9
; Relative dielectric constant for the Cut-off or DC of the reaction field
epsilon-r= 78
; Method for doing Van der Waals
vdw-type = User
; cut-off lengths
rvdw-switch  = 0
rvdw = 0.9
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension  = 1
; Seperate tables between energy group pairs
energygrp_table  =
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
; EWALD/PME/PPPM parameters
pme_order= 4
ewald_rtol   = 1e-05
ewald_geometry   = 3d
epsilon_surface  = 0
optimize_fft = no

; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm = Still
; Frequency of calculating the Born radii inside rlist
nstgbradii   = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii = 2
; Salt concentration in M for Generalized Born models
gb_saltconc  = 0

; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)
implicit_solvent = No

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl   = berendsen
; Groups to couple separately
tc-grps  = System
; Time constant (ps) and reference temperature (K)
tau_t= 0.1
ref_t= 300
; Pressure coupling
Pcoupl   = no
Pcoupltype   = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p= 0.5
compressibility  = 4.5e-5
ref_p= 1.0
; Random seed for Andersen thermostat
andersen_seed= 815131


Can anyone of you tell me what is the reason for that?

Thank you in advance.

Yang

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RE: [gmx-users] mdp file

[He, Yang]

Hi Mark,

This is what I got when I use the command gmxcheck:

Checking file traj.trr
trn version: GMX_trn_file (single precision)
Reading frame   0 time0.000
# Atoms  34
Last frame  1 time0.100


Item#frames Timestep (ps)
Step 20.1
Time 20.1
Lambda   20.1
Coords   20.1
Velocities   20.1
Forces   0
Box  20.1

Also, I have tried to increase  the value of nsteps to 1, but no change 
happened still just the static figure.

I really got stuck about that.

Hope to get your further suggestions,

Thank you .

Yang



From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Mark Abraham [EMAIL 
PROTECTED]
Sent: Thursday, November 06, 2008 3:52 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] mdp file

He, Yang wrote:
> Hi all users,
>
> When I use the command "mdrun -tablep table.xvg " to run my model in gromacs, 
>  it always shows that:
>
> starting mdrun 'DNA in water'
> 1 steps, 20.0 ps.

This is orders of magnitude too short to expect a large conformational
change to happen. Think nanoseconds at least. Depending on the number of
base pairs, think much more than that. You should be aware of how long
this might take, since you've read some literature about MD on DNA, right?

> Warning: 1-4 interaction between 11 and 19 at distance 1.437 which is larger 
> than the 1-4 table size 1.000 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

Don't ignore warnings unless you know what they mean and it's OK. See
http://wiki.gromacs.org/index.php/Errors#1-4_interaction_not_within_cut-off

> And no more information . Furthermore, I use the command ngmx to look at the 
> trajectory , I found that  only when I set the value of nsteps by 10,  will 
> there be little animation about my DNA two strands' disassociation . While I 
> try to reduce the value of dt , nstdisreout , nstorireout and nstdihreout , 
> it also did not work and I can not see any disassociation of DNA strands  
> using the command "ngmx".

Probably, you only wrote one frame before it crashed. Does the log file
look like it terminated normally after 1 steps? Use gmxcheck to see
how many frames you have in the trajectory file.

> Also, what I got confused is that when I set the value of nsteps larger than 
> 10, there is just static figure about DNA model.  This is my part of mdp file

1) You need the simulation not to crash
2) You need to simulate for long enough (nsteps) to see a change
3) You need to write output (nstxout or nstxtcout) sufficiently often to
keep yourself happy.

Mark
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[gmx-users] mdp file

[He, Yang]

Hi all users,

When I use the command "mdrun -tablep table.xvg " to run my model in gromacs,  
it always shows that:

starting mdrun 'DNA in water'
1 steps, 20.0 ps.

Warning: 1-4 interaction between 11 and 19 at distance 1.437 which is larger 
than the 1-4 table size 1.000 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

And no more information . Furthermore, I use the command ngmx to look at the 
trajectory , I found that  only when I set the value of nsteps by 10,  will 
there be little animation about my DNA two strands' disassociation . While I 
try to reduce the value of dt , nstdisreout , nstorireout and nstdihreout , it 
also did not work and I can not see any disassociation of DNA strands  using 
the command "ngmx".

Also, what I got confused is that when I set the value of nsteps larger than 
10, there is just static figure about DNA model.  This is my part of mdp file

; Start time and timestep in ps
tinit= 0
dt   = 0.002
nsteps   = 1
; For exact run continuation or redoing part of a run
init_step= 0
; mode for center of mass motion removal
comm-mode= Linear
; number of steps for center of mass motion removal
nstcomm  = 1
; group(s) for center of mass motion removal
comm-grps=




; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist  = 10
; ns algorithm (simple or grid)
ns_type  = grid
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc  = xyz
; nblist cut-off
rlist= 0.686
domain-decomposition = no

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = User
rcoulomb-switch  = 0
rcoulomb = 0.9
; Relative dielectric constant for the Cut-off or DC of the reaction field
epsilon-r= 78
; Method for doing Van der Waals
vdw-type = User
; cut-off lengths
rvdw-switch  = 0
rvdw = 0.9
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension  = 1
; Seperate tables between energy group pairs
energygrp_table  =
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
; EWALD/PME/PPPM parameters
pme_order= 4
ewald_rtol   = 1e-05
ewald_geometry   = 3d
epsilon_surface  = 0
optimize_fft = no

; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm = Still
; Frequency of calculating the Born radii inside rlist
nstgbradii   = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii = 2
; Salt concentration in M for Generalized Born models
gb_saltconc  = 0

; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)
implicit_solvent = No

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl   = berendsen
; Groups to couple separately
tc-grps  = System
; Time constant (ps) and reference temperature (K)
tau_t= 0.1
ref_t= 300
; Pressure coupling
Pcoupl   = no
Pcoupltype   = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p= 0.5
compressibility  = 4.5e-5
ref_p= 1.0
; Random seed for Andersen thermostat
andersen_seed= 815131


Any idea about this problem? any suggestions will be highly appreciated .

Thank you .

Yang
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RE: [gmx-users] the mdp file

[He, Yang]

Hi Justin,

I have changed the value of nsteps(>100) and the nstout(=1), but I found that 
there is just the static figure and no animation .

it always shows that :Last frame  0 time0.000

What is the problem?

Thank you for your reply.

Yang

From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Justin A. Lemkul [EMAIL 
PROTECTED]
Sent: Monday, November 03, 2008 4:22 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] the mdp file

He, Yang wrote:
> Hi all users,
>
> When I change the value of nsteps in my mdp file to run the gromacs and show 
> the trajectory in the gromcas, I found that only the value of nsteps is set 
> by 10, is there just  the animation of the molecule's movement . I have tried 
> many time and set the other values of nsteps, there isn't any movement about 
> the molecule at all.
>

I'm not quite clear on what the problem is.  But you should be aware that 10
steps (0.02 ps in your case!) is an exceedingly short timeframe under any
circumstances.

If what you've shown is your full .mdp file, then the other values will be taken
as default.  For output (nstxout) this value is 100.  So you will likely only
see the starting and ending coordinates of your 10-step simulation.

Try a longer simulation (>100 steps) or specify nstxout = 1 and see if you
generate 10 frames.

-Justin

> I am strange about that and this is my part of mdp file:
>
> ;VARIOUS PREPROCESSING OPTIONS
> title= atom
> ; Preprocessor - specify a full path if necessary.
> cpp  = cpp
> define   =
>
> ; RUN CONTROL PARAMETERS
> integrator   = md
> ; Start time and timestep in ps
> tinit= 0
> dt   = 0.002
> nsteps   = 10
> ; For exact run continuation or redoing part of a run
> init_step= 0
> ; mode for center of mass motion removal
> comm-mode= Linear
> ; number of steps for center of mass motion removal
> nstcomm  = 1
> ; group(s) for center of mass motion removal
> comm-grps=
>
>
>
>
> ; NEIGHBORSEARCHING PARAMETERS
> ; nblist update frequency
> nstlist  = 1
> ; ns algorithm (simple or grid)c 4
> ns_type  = grid
> ; Periodic boundary conditions: xyz (default), no (vacuum)
> ; or full (infinite systems only)
> pbc  = xyz
> ; nblist cut-off
> rlist= 0.686
> domain-decomposition = no
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> ; Method for doing electrostatics
> coulombtype  = User
> rcoulomb-switch  = 0
> rcoulomb = 0.9
> ; Relative dielectric constant for the Cut-off or DC of the reaction field
> epsilon-r= 78
> ; Method for doing Van der Waals
> vdw-type = User
> ; cut-off lengths
> rvdw-switch  = 0
> rvdw = 0.9
> ; Apply long range dispersion corrections for Energy and Pressure
> DispCorr = EnerPres
> ; Extension of the potential lookup tables beyond the cut-off
> table-extension  = 1
> ; Seperate tables between energy group pairs
> energygrp_table  =
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing   = 0.12
> ; FFT grid size, when a value is 0 fourierspacing will be used
> fourier_nx   = 0
> fourier_ny   = 0
> fourier_nz   = 0
> ; EWALD/PME/PPPM parameters
> pme_order= 4
> ewald_rtol   = 1e-05
> ewald_geometry   = 3d
> epsilon_surface  = 0
> optimize_fft = no
>
>
> Can anyone of you tell me what is the problem?
>
> Thank you very much.
>
> Yang
> ___
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>

--


Justin A. Lemkul
Graduate Research Assistant
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] the mdp file

[He, Yang]

Hi all users,

When I change the value of nsteps in my mdp file to run the gromacs and show 
the trajectory in the gromcas, I found that only the value of nsteps is set by 
10, is there just  the animation of the molecule's movement . I have tried many 
time and set the other values of nsteps, there isn't any movement about the 
molecule at all.

I am strange about that and this is my part of mdp file:

;VARIOUS PREPROCESSING OPTIONS
title= atom
; Preprocessor - specify a full path if necessary.
cpp  = cpp
define   =

; RUN CONTROL PARAMETERS
integrator   = md
; Start time and timestep in ps
tinit= 0
dt   = 0.002
nsteps   = 10
; For exact run continuation or redoing part of a run
init_step= 0
; mode for center of mass motion removal
comm-mode= Linear
; number of steps for center of mass motion removal
nstcomm  = 1
; group(s) for center of mass motion removal
comm-grps=




; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist  = 1
; ns algorithm (simple or grid)c 4
ns_type  = grid
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc  = xyz
; nblist cut-off
rlist= 0.686
domain-decomposition = no

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = User
rcoulomb-switch  = 0
rcoulomb = 0.9
; Relative dielectric constant for the Cut-off or DC of the reaction field
epsilon-r= 78
; Method for doing Van der Waals
vdw-type = User
; cut-off lengths
rvdw-switch  = 0
rvdw = 0.9
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension  = 1
; Seperate tables between energy group pairs
energygrp_table  =
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
; EWALD/PME/PPPM parameters
pme_order= 4
ewald_rtol   = 1e-05
ewald_geometry   = 3d
epsilon_surface  = 0
optimize_fft = no


Can anyone of you tell me what is the problem?

Thank you very much.

Yang
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[gmx-users] pdb file

[He, Yang]

Hi all users,

I just encountered a problem about the DNA model when I set the coordinate in 
the pdb file . It always shows very strange figure about the DNA model.

My pdb file is like this:

ATOM  1  Ab1  DNA  1 0.0510.575 0.516   1.0  0.0
ATOM  2  Tb1  DNA  1 0.1910.159 2.344   1.0  0.0
ATOM  3  S1   DNA  1 1.2802.365 6.568   1.0  0.0
ATOM  4  S2   DNA  1 1.280   -2.365-6.568   1.0  0.0
ATOM  5  P1   DNA  1 2.186   -0.628 8.896   1.0  0.0
ATOM  6  P2   DNA  1 2.186   -0.628-8.896   1.0  0.0
ATOM  7  S3   DNA  1 4.660   -1.947 6.704   1.0  0.0
ATOM  8  S4   DNA  1 4.6601.947-6.704   1.0  0.0
ATOM  9  Cb1  DNA  1 3.4310.162 0.756   1.0  0.0
ATOM 10  Gb1  DNA  1 3.571   -1.249 1.989   1.0  0.0
ATOM 11  P3   DNA  1 5.556   -5.737 6.828   1.0  0.0
ATOM 12  P4   DNA  1 5.5565.737-6.828   1.0  0.0
ATOM 13  S5   DNA  1 8.040   -5.516 4.279   1.0  0.0
ATOM 14  S6   DNA  1 8.0405.516-4.279   1.0  0.0
ATOM 15  Gb2  DNA  1 6.811   -1.814 1.407   1.0  0.0
ATOM 16  Cb2  DNA  1 6.951   -0.319 0.764   1.0  0.0
ATOM 17  P5   DNA  1 8.936   -8.655 2.152   1.0  0.0
ATOM 18  P6   DNA  1 8.9368.655-2.152   1.0  0.0
ATOM 19  S7   DNA  1 11.426.978 0.220   1.0  0.0
ATOM 20  S8   DNA  1 11.42   -6.978-0.220   1.0  0.0
ATOM 21  Tb2  DNA  1 10.191  -0.707 0.430   1.0  0.0
ATOM 22  Ab2  DNA  1 10.331  -2.237-0.518   1.0  0.0
CONECT  1  3
CONECT  2  4
CONECT  3  1  5
CONECT  4  2  6
CONECT  5  3  7
CONECT  6  4  8
CONECT  7  5  9  11
CONECT  8  6 10  12
CONECT  9  7
CONECT 10  8
CONECT 11  7  13
CONECT 12  8  14
CONECT 13  11  15  17
CONECT 14  12  16  18
CONECT 15  13
CONECT 16  14
CONECT 17  13  19
CONECT 18  14  20
CONECT 19  17  21
CONECT 20  18  22
CONECT 21  19
CONECT 22  20
MASTER00000000   22022 0
END

Can anyone of you tell me whether there is something wrong with my pdb file?

Thank you.

Yang
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[gmx-users] table use

[He, Yang]

Hi all users,

When I input the mdrun -table table_nonbond.xvg

it always shows that :

Fatal error:
Library file tablep.xvg not found in current dir nor in default directories.
(You can set the directories to search with the GMXLIB path variable)

Has anyone encountered the same problem? Can you share me your experience about 
how to solve it ?

Thank you very much.

Yang
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RE: [gmx-users] table command

[He, Yang]

Hi Mark,

Sorry to bother you again. I just change my table file a little by adding more 
values into the file and then I use the command;

mdrun -table table_nonbond.xvg

it shows :

Fatal error:
Library file tablep.xvg not found in current dir nor in default directories.
(You can set the directories to search with the GMXLIB path variable)
What is the problem?

Yang

From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Mark Abraham [EMAIL 
PROTECTED]
Sent: Monday, October 27, 2008 3:48 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] table command

He, Yang wrote:
> Hi all users,
>
> I just use the command  mdrun -table table_nonbond.xvg  to run the table file 
> but it always shows that
>
> Fatal error:
> Tables in file table_nonbond.xvg not long enough for cut-off:
> should be at least 1.90 nm
> Actually, I have listed all the values up to 2.000nm in the file so I get a 
> little confused about this error;
>
> Can anyone of you give me some suggestions?

Compare your file with the ones in the distribution in
share/gromacs/top/*xvg, or with those generated with mdrun -debug
without attempting to use your own table.

Mark
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RE: [gmx-users] table_bonded.xvg

[He, Yang]

Hi ,

I also encountered the same problem when I use the command:

 mdrun -table table_nonbond.xvg

it shows that

Fatal error:
Library file bond_b0_b0.xvg not found in current dir nor in default
directories.
(You can set the directories to search with the GMXLIB path variable)

I wonder whether you have figured out this problem. Would you mind share your 
experience?

Thank you .

Yang

From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of A.Rzepiela [EMAIL 
PROTECTED]
Sent: Monday, October 27, 2008 2:47 AM
To: gmx-users@gromacs.org
Subject: [gmx-users] table_bonded.xvg

Hi,

When I type :

mdrun  -tableb bond_b0.xvg -v

I get following message:

  Program mdrun, VERSION 4.0
Source code file: futil.c, line: 527

Fatal error:
Library file bond_b0_b0.xvg not found in current dir nor in default
directories.
(You can set the directories to search with the GMXLIB path variable)
---

Thats what confused me


when I type mdrun  -tableb
It reads table_b0.xvg

Greetings

Andrzej


> Hi,
>
> According to me it does not.
> I never change the default names.
> But with the default names the table file name option is "table.xvg"
> and for a tabulated bond table number 0, it correctly opens "table_b0.xvg"
>
> Berk


>> From: A.Rzepiela at rug.nl
>> To: gmx-users at gromacs.org
>> Date: Fri, 24 Oct 2008 13:45:53 +0200
>> Subject: [gmx-users] table_bonded.xvg
>>
>> Dear Users
>>
>> In gromacs 4.0, in file force.c  in function make_bonded_tables line
>> (1007)
>>   sprintf(tabfn + strlen(basefn)  - strlen(ftp2ext(efXVG)) -
>> 1,"_%s%d.%s", tabext, i, ftp2ext(efXVG));
>>
>> produces table_bonded_bonded.xvg  instead of  table_bonded.xvg
>>
>> Greetings
>>
>> Andrzej Rzepiela
>> ___
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[gmx-users] table command

[He, Yang]

Hi all users,

I just use the command  mdrun -table table_nonbond.xvg  to run the table file 
but it always shows that

Fatal error:
Tables in file table_nonbond.xvg not long enough for cut-off:
should be at least 1.90 nm
Actually, I have listed all the values up to 2.000nm in the file so I get a 
little confused about this error;

Can anyone of you give me some suggestions?

Thank you in advance.

Yang
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RE: [gmx-users] Fatal error: Invalid dihedral type 0

[He, Yang]

Hi Mark,

I have tried a lot but it  still did not work. I just ran a similar case whose 
file content is similar to what I have right now  and it worked , while this 
always failed.

I will post what I have to you.

Thank you for your help.

Yang



From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Mark Abraham [EMAIL 
PROTECTED]
Sent: Saturday, October 25, 2008 10:37 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Fatal error:  Invalid dihedral type 0

He, Yang wrote:
> Hi Mark,
>
> I have carefully adjusted the parameters but it still doesn't work. I am 
> confused about that because I just dealt with the dihedraltypes before in the 
> same way and it works while for this time, something wrong happened.

Try reading all of the grompp output carefully - paying attention to
warnings, etc. This error message can arise because you've mangled
something elsewhere in the .top file and the parser gets lost. If all
else fails, please post your full command line, the full output of
grompp, your full .mdp file and your full .top file.

Mark
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atom.gro
Description: atom.gro


att.mdp
Description: att.mdp


hust.top
Description: hust.top


ffyxhbon.itp
Description: ffyxhbon.itp


ffyxhnb.itp
Description: ffyxhnb.itp
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RE: [gmx-users] Fatal error: Invalid dihedral type 0

[He, Yang]

Hi Mark,

I have carefully adjusted the parameters but it still doesn't work. I am 
confused about that because I just dealt with the dihedraltypes before in the 
same way and it works while for this time, something wrong happened.

Could you give me more suggestions about this/

Thank you

Yang

From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Mark Abraham [EMAIL 
PROTECTED]
Sent: Saturday, October 25, 2008 4:50 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Fatal error:  Invalid dihedral type 0

He, Yang wrote:
> Hi  all users,
>
> I just use the grompp -f att.mdp -c atom_b4em.gro -p hust.top -maxwarn 10 -pp 
> and then always show the :
>
>
> Fatal error:
> Invalid dihedral type 0

You should try to work out which line this relates to...

> [ dihedraltypes ]
>   ; ilfunc q0  cq
> Ab   SLb   2 0.000   -22.60
>
>
>
> [ dihedraltypes ]
> ;j k   func phi0 cp   mult
>  SRa   P   1180.   -33.422
>
>
> I have tried  but it did not  work .

Yup - read the format description for these function types (e.g. Table
5.3 in the 3.3 manual). You're giving a set of parameters that do not
match your function types.

Mark
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[gmx-users] Fatal error: Invalid dihedral type 0

[He, Yang]

Hi  all users,

I just use the grompp -f att.mdp -c atom_b4em.gro -p hust.top -maxwarn 10 -pp 
and then always show the :


Fatal error:
Invalid dihedral type 0

and this is my bon.itp file;

[ bondtypes ]
  ; ij  funcb0  kb
Ab   SLa  1 0.6430   374468
Tb   SRa  1 0.4880   502080
SLa   P   1 0.3559   376560
SRb   P   1 0.3899   418400
HW   OW   1 0.1  418400


[ angletypes ]
  ; ijk   func   th0 cth
Ab   SLa  P 1 94.49   334.72
Tb   SRa  P 1 112.72  284.51
SLa   P  SLb1 94.49   334.72
SRa   P  SRb1 94.49   334.72
HW   OW  HW1 109.500 502.080


[ dihedraltypes ]
  ; ilfunc q0  cq
Ab   SLb   2 0.000   -22.60



[ dihedraltypes ]
;j k   func phi0 cp   mult
 SRa   P   1180.   -33.422


I have tried  but it did not  work .

Can anyone of you give me some suggestions about that/

Thank you in advance.

Yang
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RE: [gmx-users] f(x) g(x) h(x)in the user defined potential functions

[He, Yang]

Hi Mark,

Thank you for your reply. From your point of view,   I wonder whether you mean 
I need to write a table based on different interaction types and then change 
the source code  for recognition when running my case in the gromacs .I just 
have no idea about that .Can you give me further suggestion about that? I am 
stuck by this point

Thank you very much.

Yang

From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Mark Abraham [EMAIL 
PROTECTED]
Sent: Thursday, October 23, 2008 6:11 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] f(x) g(x) h(x)in the user defined potential functions

He, Yang wrote:
> Hi all users,
>
> When I am defining the user potential functions using the table, I 
> encountered a problem that there are several unstable parameters  in the 
> separate f(x),g(x),h(x) .For example, in the g(x), there is a parameter 
> "epsilon" whose value will depend on different pairs.In this situation, I can 
> not get a specific value in the table file . I don't know how to solve this 
> problem.
>
> Can anyone of you give me some suggestions about that?

So your nonbonded interaction depends on your atom types. You could
write a table for each interaction type, modify GROMACS to read them all
in, and then modify the routine that calls the kernels to use the
correct one. This additional memory usage would grow as the square of
the number of atom types. You would also see some performance loss which
you could minimize by arranging to evaluate all of one type of nonbonded
interaction close together in the nonbonded routines, to minimize cache
misses.

Better would be if some of these functions (conveniently) differed only
by a multiplicative or additive constant so that you could re-use the
same table and then apply a correction function, but you'll have to look
at your own maths for that.

Mark
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[gmx-users] f(x) g(x) h(x)in the user defined potential functions

[He, Yang]

Hi all users,

When I am defining the user potential functions using the table, I encountered 
a problem that there are several unstable parameters  in the separate 
f(x),g(x),h(x) .For example, in the g(x), there is a parameter "epsilon" whose 
value will depend on different pairs.In this situation, I can not get a 
specific value in the table file . I don't know how to solve this problem.

Can anyone of you give me some suggestions about that?

Thank you in advance.

Yang
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RE: [gmx-users] how to use the new potential

[He, Yang]

Hi Mark,

Thank you for your reply. I will follow your suggestions and have a try.

Hope to get further help

Regards,

Yang

From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Matthew Hoopes [EMAIL 
PROTECTED]
Sent: Wednesday, October 22, 2008 5:41 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] how to use the new potential

>He, Yang wrote:
>> Hi all users,
>>
>> I am engaged in deal with the course grain model,in which the
>> potential functions are not the same as in gromacs.Hence, If I want to
>> use the new potentials , I guess I can change the source code or use
>> the table. But I never have this experience about  that.Can anyone of
>> you give me some suggestions or examples?
>
>Start with the manual. :-) Hopefully the version 4 manual will be out
>soon, but even if not, the 3.3 manual will be fine for nonbonded
>tabulated potentials.
>
>Mark

Here is an example:

#
# Tabulated WCA potentials, dr=0.002, rc=3.5, no coulomb
#
0.00e+00  0.00e+00  0.00e+00  0.00e+00
0.00e+00  0.00e+00  0.00e+00
2.00e-03  0.00e+00  0.00e+00  0.00e+00
0.00e+00  0.00e+00  0.00e+00
...
3.60e-02  0.00e+00  0.00e+00  0.00e+00
0.00e+00  0.00e+00  0.00e+00
3.80e-02  0.00e+00  0.00e+00  0.00e+00
0.00e+00  0.00e+00  0.00e+00
4.00e-02  0.00e+00  0.00e+00  0.00e+00
0.00e+00  2.3841857812e+17  7.1525573584e+19
4.20e-02  0.00e+00  0.00e+00  0.00e+00
0.00e+00  1.3276038530e+17  3.7931538762e+19
4.40e-02  0.00e+00  0.00e+00  0.00e+00
0.00e+00  7.5967506265e+16  2.0718410875e+19
4.60e-02  0.00e+00  0.00e+00  0.00e+00
0.00e+00  4.4562136749e+16  1.1624905294e+19
...
3.498000e+00  0.00e+00  0.00e+00  0.00e+00
0.00e+00  0.00e+00  0.00e+00
3.50e+00  0.00e+00  0.00e+00  0.00e+00
0.00e+00  0.00e+00  0.00e+00

Column 1) is r (distance between atoms) 6) h(r) the repulsive term of the
potential and 7) -h'(r) as defined in section 6.7.2

1) Just use your favorite script (I used octave) to generate the following
text file with printf statements or something similar.
2) If some of the early values are too large, it may cause an error so I
just zeroed them out.
3) The information you need is in a few places in the manual. The table
above is defined in section 6.7.2 on page 131 of the GROMACS 4.0 manual.
4) You will also want to read section 7.3.12 on page 148 about entries in
your parameter file (e.g. energy groups, table file naming conventions)
5) You will need an index file that has particle groups for your new
potentials. The group names in the index file are what you use for energy
groups.
6) Pay attention to which combination rules you use in the topology file
7) Note that in the LJC(12-6-1) table in the top directory of GROMACS, the
minimum of the LJ is -0.25 and not -1.0 so I guess there is a factor of
4*epsilon multiplied to the table values.

What I don't know, and perhaps someone else can answer this is what should
be done if you are unsure of how your potential is separated in to
attractive and repulsive terms (e.g. LJ with COS tail). First, it's
piecewise, and second the COS section is not the sum of two terms so how
should it be broken across g(r) and h(r) or is it always OK to use the g(r)
column for the whole potential?

Hope this helps.

-Matt

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[gmx-users] how to use the new potential

[He, Yang]

Hi all users,

I am engaged in deal with the course grain model,in which the potential 
functions are not the same as in gromacs.Hence, If I want to use the new 
potentials , I guess I can change the source code or use the table. But I never 
have this experience about  that.Can anyone of you give me some suggestions or 
examples?

Thank you in advance.

Yang
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RE: [gmx-users] modify bondfree.c and recompile

[He, Yang]

Hi David,


Thank you for your reply. As for the new non-bond potential, if I want to use 
the gromacs to deal with them, what should i do in the gromacs? Do you have any 
suggestions about that? Change the source code?

Thank you for your help.

Regard,

Yang

From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of David van der Spoel 
[EMAIL PROTECTED]
Sent: Tuesday, October 21, 2008 11:09 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] modify bondfree.c and recompile

He, Yang wrote:
> Hi Jian,
>
> Do you also need to change the source code to get a new potential function? I 
> am also engaged in this job. DO you have any experience about this job?
>
>
You can use tables for bonded potentials as well, without changing any code.

> Regards,
>
> Yang
> 
> From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Jian Zou [EMAIL 
> PROTECTED]
> Sent: Tuesday, October 21, 2008 7:24 AM
> To: [EMAIL PROTECTED]; gmx-users@gromacs.org
> Subject: [gmx-users] modify bondfree.c and recompile
>
> Hi,
>
> If I only change some functional form in bondfree.c (the number of
> parameters are kept the same), can I just do "make mdrun" and "make
> install-mdrun" to recompile from the source?
>
> I cannot find the dependency between the source files and the Gromacs
> utilities (grompp and mdrun).
>
> I compare the tpr file generated before and after the change and they
> are the same. Therefore it seems to me that grompp does not read the
> formulation of bonded interactions, am I right?
>
> Thank you very much for the reply.
>
>
> Regards,
>
> Jian
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--
David.

David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED][EMAIL PROTECTED]   http://folding.bmc.uu.se

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RE: [gmx-users] modify bondfree.c and recompile

[He, Yang]

Hi Jian,

Do you also need to change the source code to get a new potential function? I 
am also engaged in this job. DO you have any experience about this job?


Regards,

Yang

From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Jian Zou [EMAIL 
PROTECTED]
Sent: Tuesday, October 21, 2008 7:24 AM
To: [EMAIL PROTECTED]; gmx-users@gromacs.org
Subject: [gmx-users] modify bondfree.c and recompile

Hi,

If I only change some functional form in bondfree.c (the number of
parameters are kept the same), can I just do "make mdrun" and "make
install-mdrun" to recompile from the source?

I cannot find the dependency between the source files and the Gromacs
utilities (grompp and mdrun).

I compare the tpr file generated before and after the change and they
are the same. Therefore it seems to me that grompp does not read the
formulation of bonded interactions, am I right?

Thank you very much for the reply.


Regards,

Jian
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RE: [gmx-users] How can I generate a Input *.gro file of coarse grain model?

[He, Yang]

Hi ,

I was also engaged in dealing with the problem about the course grain model . I 
find that in this CG force field , the potential functions almost don't 
correspond to that in the gromacs.

Hence, I wonder whether you know to how to define these new potential functions.

Thank you in advance.

Yang

From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of xuji [EMAIL PROTECTED]
Sent: Sunday, October 19, 2008 1:47 AM
To: gmx-users@gromacs.org
Subject: [gmx-users] How can I generate a Input *.gro file of coarse grain  
model?

Dear all gromacs users:

I am trying to use the MARTINI CG force field from Marrink et al. in my 
simulation.
But I don't konw how to generate the input *.gro files.
When I use all-atom model, in gromacs I can use "genbox" "editconf" et al to 
generate
the input *.gro files. For example, I can use "genbox -cs -box 10 10 10 -o 
waterbox.gro"
to generate pure water box. But if I only have the files downloaded from
"http://md.chem.rug.nl/~marrink/MARTINI/Parameters.html"; , and I use a *.top 
file
which contains:

#include "martini_v2.0.itp"
#include "martini_v2.0_lipids.itp"

[ system ]
DPPC BILAYER

[ molecules ]
DPPC 128
W 2000

Can I generate a *.gro file according to this topology file using Gromacs' 
tools?
If can, how do it?

Appreciate any help in advance!




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[gmx-users] coulombic

[He, Yang]

Hi all users,

I just got confused about whether I need to input the values of the coulombic 
interaction in the nb.itp file .If not, I wonder how the gromacs will recognize 
the coulombic interaction ,in the mdp.file?

Sorry for this dull question.

Thank you in advance.

Yang
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[gmx-users] how to define the potential function in the course grain model

[He, Yang]

Hi all users,

Now I am using the gromacs to simulating the course model  for DNA but I find 
that the potential functions in this model are not found in the gromacs force 
field .  Can anyone tell me how to define these new potential functions in the 
gromacs files?

The form fro the new potential functions are shown in the attachment.

Thank you in advance.

Yang

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RE: [gmx-users] transfer pdb to gro

[He, Yang]

Hi Justin,

Thank you for your reply. I have followed the regular forms about pdb file but 
it still shows that :

___> Opening library file /usr/share/gromacs/top/aminoacids.dat
> Opening library file /usr/share/gromacs/top/atommass.dat
> Opening library file /usr/share/gromacs/top/vdwradii.dat
> Opening library file /usr/share/gromacs/top/dgsolv.dat
> #Entries in atommass.dat: 82 vdwradii.dat: 26 dgsolv.dat: 7
> Warning: Number of atoms in atom.pdb is 0
> WARNING: all CONECT records are ignored
> Read 0 atoms
> Volume: 0 nm^3, corresponds to roughly 0 electrons
> No velocities found
>
So I think it is because that the atom types such as Sugar ,Adenine base are 
not recognized  by the gromacs .Also, what I want to solve is that how to 
define these big atoms .

Do you know how to define these big atoms in order to make the gromacs  
recognize them and creat the correct gro.file

Thank you .

Yang
From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Justin A. Lemkul [EMAIL 
PROTECTED]
Sent: Wednesday, October 15, 2008 4:36 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] transfer pdb to gro

He, Yang wrote:
> Hi all users,
>
> When I use the editconf command to transform pdb file to gro file, it shows 
> like this
>
> Opening library file /usr/share/gromacs/top/aminoacids.dat
> Opening library file /usr/share/gromacs/top/atommass.dat
> Opening library file /usr/share/gromacs/top/vdwradii.dat
> Opening library file /usr/share/gromacs/top/dgsolv.dat
> #Entries in atommass.dat: 82 vdwradii.dat: 26 dgsolv.dat: 7
> Warning: Number of atoms in atom.pdb is 0
> WARNING: all CONECT records are ignored
> Read 0 atoms
> Volume: 0 nm^3, corresponds to roughly 0 electrons
> No velocities found
>
> And this is my original pdb file
>
>  ATOM   1  Ab   DNA   0.5750.516 0.051   1.0  0.0
>  ATOM   2  Tb   DNA   0.1592.344 0.191   1.0  0.0
>  ATOM   3  S1   DNA   2.3656.568 1.280   1.0  0.0
>  ATOM   4  S2   DNA   2.365   -6.568-1.280   1.0  0.0
>  ATOM   5  P1   DNA   -0.628   8.896 2.186   1.0  0.0
>  ATOM   6  P2   DNA   -0.628  -8.896-2.186   1.0  0.0
>  ATOM   7  S3   DNA  -1.9476.704-4.660   1.0  0.0
>  ATOM   8  S4   DNA  -1.947   -6.704 4.660   1.0  0.0
> CONECT  1  3
> CONECT  2  4
> CONECT  3  1  5
> CONECT  4  2  6
> CONECT  5  3  7
> CONECT  6  4  8
> CONECT  7  5
> CONECT  8  6
> MASTER00000000   80   80
> END
>
> not very complex, only 8 atoms .  And I find these atoms are not included in 
> the gromacs so i defined them in the .atp file this
>
>  Ab  134.1;   Adenine base of DNA
>  Tb  125.1;   Thymine base of DNA
>  S   83.11;   Sugar of DNA
>  P   94.97;   Phosphate of DNA
>
>

The .atp file means nothing for editconf.

>  Can anyone of you help me sovle this problem?
>

It looks like the formatting of your .pdb file is irregular.  A fixed format is
required for proper detection of atoms and coordinates.  See here:

http://www.wwpdb.org/docs.html

-Justin

> Thank you in advance
>
> Yang He
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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--


Justin A. Lemkul
Graduate Research Assistant
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] transfer pdb to gro

[He, Yang]

Hi all users,

When I use the editconf command to transform pdb file to gro file, it shows 
like this

Opening library file /usr/share/gromacs/top/aminoacids.dat
Opening library file /usr/share/gromacs/top/atommass.dat
Opening library file /usr/share/gromacs/top/vdwradii.dat
Opening library file /usr/share/gromacs/top/dgsolv.dat
#Entries in atommass.dat: 82 vdwradii.dat: 26 dgsolv.dat: 7
Warning: Number of atoms in atom.pdb is 0
WARNING: all CONECT records are ignored
Read 0 atoms
Volume: 0 nm^3, corresponds to roughly 0 electrons
No velocities found

And this is my original pdb file

 ATOM   1  Ab   DNA   0.5750.516 0.051   1.0  0.0
 ATOM   2  Tb   DNA   0.1592.344 0.191   1.0  0.0
 ATOM   3  S1   DNA   2.3656.568 1.280   1.0  0.0
 ATOM   4  S2   DNA   2.365   -6.568-1.280   1.0  0.0
 ATOM   5  P1   DNA   -0.628   8.896 2.186   1.0  0.0
 ATOM   6  P2   DNA   -0.628  -8.896-2.186   1.0  0.0
 ATOM   7  S3   DNA  -1.9476.704-4.660   1.0  0.0
 ATOM   8  S4   DNA  -1.947   -6.704 4.660   1.0  0.0
CONECT  1  3
CONECT  2  4
CONECT  3  1  5
CONECT  4  2  6
CONECT  5  3  7
CONECT  6  4  8
CONECT  7  5
CONECT  8  6
MASTER00000000   80   80
END

not very complex, only 8 atoms .  And I find these atoms are not included in 
the gromacs so i defined them in the .atp file this

 Ab  134.1;   Adenine base of DNA
 Tb  125.1;   Thymine base of DNA
 S   83.11;   Sugar of DNA
 P   94.97;   Phosphate of DNA


 Can anyone of you help me sovle this problem?

Thank you in advance

Yang He
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RE: [gmx-users] gromacs

[He, Yang]

Hello Justin,

Thank you for your reply. I am using the gromacs to simulate a case about the 
course grain for DNA. This case includes some superatoms in the course grain 
force field and I have defined the superatoms in the .atp files and the atoms 
type in the water like this:
 Ab  134.1;   Adenine base of DNA
 Tb  125.1;   Thymine base of DNA
 S   83.11;   Sugar of DNA
 P   94.97;   Phosphate of DNA
 OW   15.99940;  water oxygen in SOL
 HW1.00800;water hydrogen  in SOL

 But it shows that Fatal error:
Atomtype 'OW' not found!
Also, this is my spc.itp file

[ moleculetype ]
; molname   nrexcl
SOL 3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass
#ifdef _FF_GROMACS
 1 OW  1SOL OW  1  -0.82
 2 HW  1SOLHW1  1   0.41
 3 HW  1SOLHW2  1   0.41
#endif
#ifdef _FF_GROMOS96
#ifdef HEAVY_H
 1 OW  1SOL OW  1  -0.829.95140
 2  H  1SOLHW1  1   0.414.03200
 3  H  1SOLHW2  1   0.414.03200
#else
 1 OW  1SOL OW  1  -0.82   15.99940
 2  H  1SOLHW1  1   0.411.00800
 3  H  1SOLHW2  1   0.411.00800
#endif
#endif
#ifdef _FF_OPLS
 1  opls_116   1SOL OW  1  -0.82
 2  opls_117   1SOLHW1  1   0.41
 3  opls_117   1SOLHW2  1   0.41
#endif

#ifdef FLEXIBLE
[ bonds ]
; i j   funct   length  force.c.
1   2   1   0.1 345000  0.1 345000
1   3   1   0.1 345000  0.1 345000

[ angles ]
; i j   k   funct   angle   force.c.
2   1   3   1   109.47  383 109.47  383


[ exclusions ]
1   2   3
2   1   3
3   1   2
#endif

Can you help me solve this problem

Thank you for your favor.

Regards,

Yang


From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Justin A. Lemkul [EMAIL 
PROTECTED]
Sent: Tuesday, October 14, 2008 12:01 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] gromacs

He, Yang wrote:
> Hi all users,
>
> I juse encountered a problem when I run the code about the course grain for 
> DNA,
>
> it shows like this
>
> creating statusfile for 1 node...
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
> checking input for internal consistency...
> calling cpp...
> In file included from ffyxh.itp:8,
>  from hust.top:11:
> ffyxhnb.itp:25:61: warning: no newline at end of file
> In file included from ffyxh.itp:9,
>  from hust.top:11:
> ffyxhbon.itp:26:5: warning: no newline at end of file
> In file included from hust.top:65:
> ffyxh.atp:6:34: warning: no newline at end of file
> hust.top:76:17: warning: no newline at end of file
> processing topology...
> Generated 32 of the 36 non-bonded parameter combinations
> ---
> Program grompp, VERSION 3.3.1
> Source code file: toputil.c, line: 61
>
> Fatal error:
> Atomtype 'OW' not found!
>
>
> I have tried to solve that , but it did not still work . So anyone of you can 
> tell me how to solve that.
>

Well, what have you done to solve it?  From the messages grompp is printing out,
it looks like the format of your files is badly mangled.  You're calling
parameters for an atomtype which does not exist within the force field you've
apparently created.  Parameters need to be defined within the .atp, *bon.itp,
and *nb.itp files for it to be recognized.

-Justin

> Thank you in advance.
>
> Yang
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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>

--


Justin A. Lemkul
Graduate Research Assistant
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] gromacs

[He, Yang]

Hi all users,

I juse encountered a problem when I run the code about the course grain for DNA,

it shows like this

creating statusfile for 1 node...

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
checking input for internal consistency...
calling cpp...
In file included from ffyxh.itp:8,
 from hust.top:11:
ffyxhnb.itp:25:61: warning: no newline at end of file
In file included from ffyxh.itp:9,
 from hust.top:11:
ffyxhbon.itp:26:5: warning: no newline at end of file
In file included from hust.top:65:
ffyxh.atp:6:34: warning: no newline at end of file
hust.top:76:17: warning: no newline at end of file
processing topology...
Generated 32 of the 36 non-bonded parameter combinations
---
Program grompp, VERSION 3.3.1
Source code file: toputil.c, line: 61

Fatal error:
Atomtype 'OW' not found!


I have tried to solve that , but it did not still work . So anyone of you can 
tell me how to solve that.

Thank you in advance.

Yang
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RE: [gmx-users] Selecting part of the trajectory

[He, Yang]

Hi all,

I am using gromacs to simulate the course grain for DNA. it is called the 
super-atoms including Phosphate (P),Sugar(S),Adenine base(Ab),Thymine(Tb). I 
have defined them in the .atp file like this,
Ab  134.1;   Adenine base
 Tb  125.1;   Thymine base
 S   83.11;   Sugar
 P   94.97;   Phosphate
But when I run this , it always shows that the atomtype "Ab" not found and  
Twin-range neighbour searching (NS) with simple NS algorithm not implemented .

I wonder whether anyone of us can tell me how to slove this problems.

In addition , I wonder how I can define the potential which is not included in 
the gromacs.

Thank you for any suggestion.

Regards,

Yang He



From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Yang Ye [EMAIL PROTECTED]
Sent: Monday, October 13, 2008 7:10 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Selecting part of the trajectory

Hi,

This is a common problem to long trajectory. It is fine as long as there is no 
real corruption in the trajectory file, caused by network, disk, etc.

Solution:
Shift a bit backward from the -b, this may be a few hundred ps or several ns, 
then extract the segment you would like to have from this secondary trajectory.

Regards,
Yang Ye


- Original Message 
From: #NGUYEN CONG TRI# <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users 
Sent: Monday, October 13, 2008 3:47:32 PM
Subject: [gmx-users] Selecting part of the trajectory

Hi all,

I want get the snapshots every 5ps of the last 1ns in a 20 ns simulation. So I 
want to cut out the last 1ns. I was able to do that using -b and -e flags of 
trjconv, say -b 19000 and -e 2 for a .trr trajectory. However, to save disk 
space I converted it into .xtc format and I cannot use trjconv with -b and -e 
flags anymore. I got error msg like:

Fatal error:
Specified frame doesn't exist or file not seekable

One more thing, my system consists of a protein and a ligand. At some 
snapshots, the ligand just jumps out of the box even when I used -pbc mol -ur 
compact. I tried with -pbc nojump and other option as well but none works 
perfectly in all cases. How to make sure that the ligand always stays with the 
protein so that I can write the script to automatically generate the snapshots 
and do some post-processing on them.

Thank you for any suggestion.

Regards,
Tri
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