[gmx-users] error in linking mopac and gromacs

[subarna thakur]

According to the suggestion I have installed the f2c package in my machine.I am 
unable to find the g2c package. I have included the f2c library by - export 
LIBS="-lmopac -lf2c". But when I running  ./configure --with-qmmm-mopac 
--disable-float , an error is comming C compiler cannot create executable. The 
config.log file shows the following section- 
onfigure:3413: checking for C compiler default output file name
configure:3440: cc -I/usr/local/include -DUSE_MOPAC -L/usr/local/lib conftest.c 
-lmopac -lf2c >&5
/usr/lib/gcc/i486-linux-gnu/4.3.3/../../../../lib/libf2c.so: undefined 
reference to `MAIN__'
collect2: ld returned 1 exit status
configure:3443: $? = 1
configure:3481: result:
configure: failed program was:
| /* confdefs.h. */ 
Please suggest a way out.Subarna Thakur

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RE: [gmx-users] git

[Dallas B. Warren]

Shouldn't you just do it anonymously?

 

git clone git://git.gromacs.org/gromacs.git

 

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the only tool you own is a hammer, every problem begins to resemble
a nail. 

 

From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Sai Pooja
Sent: Friday, 18 June 2010 3:28 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] git

 

Thanks Justin. I installed git first and then used git clone
g...@git.gromacs.org:gromacs.git and this is what I get

 

Initialized empty Git repository in /fs/home/sm868/gromacs/.git/

The authenticity of host 'git.gromacs.org (130.237.163.208)' can't be
established.

RSA key fingerprint is ef:9e:30:0e:8c:3c:70:27:c9:d5:10:26:3e:4d:a7:08.

Are you sure you want to continue connecting (yes/no)? yes

Warning: Permanently added 'git.gromacs.org,130.237.163.208' (RSA) to
the list of known hosts.

g...@git.gromacs.org's password: 

 

1) Empty repository - what does that mean?

2) What password do I need to enter here?

 

Pooja

 

On Thu, Jun 17, 2010 at 10:31 PM, Justin A. Lemkul 
wrote:



Sai Pooja wrote:

Hi,
 This is the first time I am using git. I tried to get started by using
- git clone git://git.gromacs.org/gromacs.git
 - command but got an error -
"command not found: git" (I have tried different versions of this
command available with the same result). I am sure this is something
extremely trivial. Can someone let me know what am I doing wrong?  


Have you actually installed git?  If so, it may just not be in your
$PATH.  If not, install it before you try to use it :)

-Justin

 

Regards
Pooja
 

-- 
Quaerendo Invenietis-Seek and you shall discover.

 

-- 


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


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Quaerendo Invenietis-Seek and you shall discover.

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Re: [gmx-users] git

[Mark Abraham]

- Original Message -
From: Sai Pooja 
Date: Friday, June 18, 2010 15:28
Subject: Re: [gmx-users] git
To: Discussion list for GROMACS users 

> Thanks Justin. I installed git first and then used git clone 
> g...@git.gromacs.org:gromacs.git and this is what I get
> Initialized empty Git repository in /fs/home/sm868/gromacs/.git/> The 
> authenticity of host 'git.gromacs.org (130.237.163.208)' can't be 
> established. > RSA key fingerprint is 
> ef:9e:30:0e:8c:3c:70:27:c9:d5:10:26:3e:4d:a7:08.> Are you sure you want to 
> continue connecting (yes/no)? yes> Warning: Permanently added 
> 'git.gromacs.org,130.237.163.208' (RSA) to the list of known hosts. > 
> g...@git.gromacs.org's password: > 
> 1) Empty repository - what does that mean?

"Empty" is what you call something before you put something in it :-)

> 2) What password do I need to enter here?

Your approach won't work unless you have a registered .ssh key for 
g...@git.gromacs.org, i.e. you have permission to write to the repository.

The first three different places I looked on the wiki for how to get the git 
repository recommended a different approach from yours. See 
http://www.gromacs.org/Developer_Zone/Git.

There's a lot of useful git help on the wiki and the web - please use it.

Mark

> On Thu, Jun 17, 2010 at 10:31 PM, Justin A. Lemkul  wrote:
 > 
 > 
>  Sai Pooja wrote:
 >  Hi,
>   This is the first time I am using git. I tried to get started by using - 
> git clone git://git.gromacs.org/gromacs.git 
>  - command but got an error - "command 
> not found: git" (I have tried different versions of this command available 
> with the same result). I am sure this is something extremely trivial. Can 
> someone let me know what am I doing wrong?  
   > 
>  Have you actually installed git?  If so, it may just not be in your $PATH.  
> If not, install it before you try to use it :)
 > 
>  -Justin
 > 
 >  Regards
>  Pooja
>   
 > 
>  -- 
>  Quaerendo Invenietis-Seek and you shall discover.
 > 
  > 
>  -- 
>  
 > 
>  Justin A. Lemkul
>  Ph.D. Candidate
>  ICTAS Doctoral Scholar
>  MILES-IGERT Trainee
>  Department of Biochemistry
>  Virginia Tech
>  Blacksburg, VA
>  jalemkul[at]vt.edu | (540) 231-9080
 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 > 
>  
>  -- 
>  gmx-users mailing listgmx-users@gromacs.org
 > http://lists.gromacs.org/mailman/listinfo/gmx-users
>  Please search the archive at http://www.gromacs.org/search before posting!
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 > 
> > 
> -- 
> Quaerendo Invenietis-Seek and you shall discover.
  > -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search 
> before posting!
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Re: [gmx-users] git

[Sai Pooja]

Thanks Justin. I installed git first and then used git clone
g...@git.gromacs.org:gromacs.git and this is what I get

Initialized empty Git repository in /fs/home/sm868/gromacs/.git/
The authenticity of host 'git.gromacs.org (130.237.163.208)' can't be
established.
RSA key fingerprint is ef:9e:30:0e:8c:3c:70:27:c9:d5:10:26:3e:4d:a7:08.
Are you sure you want to continue connecting (yes/no)? yes
Warning: Permanently added 'git.gromacs.org,130.237.163.208' (RSA) to the
list of known hosts.
g...@git.gromacs.org's password:

1) Empty repository - what does that mean?
2) What password do I need to enter here?

Pooja


On Thu, Jun 17, 2010 at 10:31 PM, Justin A. Lemkul  wrote:

>
>
> Sai Pooja wrote:
>
>> Hi,
>>  This is the first time I am using git. I tried to get started by using -
>> git clone git://git.gromacs.org/gromacs.git <
>> http://git.gromacs.org/gromacs.git> - command but got an error - "command
>> not found: git" (I have tried different versions of this command available
>> with the same result). I am sure this is something extremely trivial. Can
>> someone let me know what am I doing wrong?
>>
>
> Have you actually installed git?  If so, it may just not be in your $PATH.
>  If not, install it before you try to use it :)
>
> -Justin
>
>
>  Regards
>> Pooja
>>
>>
>> --
>> Quaerendo Invenietis-Seek and you shall discover.
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/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
>



-- 
Quaerendo Invenietis-Seek and you shall discover.
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Re: [gmx-users] Enough hydration of the channel

[Aswathy]

Thanks a lot.

On Fri, Jun 18, 2010 at 9:30 AM, Justin A. Lemkul  wrote:

>
>
> Aswathy wrote:
>
>> Thank you very much.
>>
>> In some papers I have seen the graph for hydration of the channel. How can
>> we calculate that using Gromacs ? (or any other program?)
>>
>
> Have a look at some of Oliver Beckstein's programs:
>
> http://sbcb.bioch.ox.ac.uk/oliver/software/
>
> There are several that might be useful to you.
>
> -Justin
>
>
>> Regards,
>> -Aswathy
>>
>>
>>
>> On Thu, Jun 17, 2010 at 7:52 PM, > chris.ne...@utoronto.ca>> wrote:
>>
>>Determining how many waters is sufficient is a tough problem, try
>>successive runs of option #3, below. As for the simpler topic of
>>getting more hydration:
>>
>>1. If the issue is simply getting the channel hydrated enough to
>>overcome some transition from dry to wet, then run a neat water box
>>od 216 spc for 100 ps and extract a frame every 10 ps, then run
>>genbox 10x successively using each of these frames. This should give
>>you massive hydration.
>>
>>2. If that doesn't work, then you could add a new equilibration step
>>where you posres some cap waters so that the channel can not dry
>>out. This may allow SC's to equilibrate to a wet environment.
>>
>>3. If the issue is that the water is still moving out, then why not
>>do SMD on a water into the pore and find out where the repulsion is.
>>
>>-- original message --
>>
>>Hi everyone,
>>
>>I have a homology model of a transporter. I want to study the ligand
>>transport through the channel. i have done the following steps.
>>
>>1. Ligand has docked to the mouth of the channel
>>2.  Inserted the complex in POPC bilayer, then solvated, and
>>equilibrated
>>for 4ns(with position restarint on Protein & ligand)
>>3. Then I saw tht there are very few wtaer inside the pore, Since this
>>channel is an aqueous pore, I have added water to the channel using
>>genbox.
>>4. Then the complete system equilibrated for pico seconds.
>>5,in order to select different snap shots for SMD (want to do a
>> multiple
>>SMDs with different starting structures.) I have run 1ns Production
>>run and
>>selected different frames.
>>
>>Suddenly I found that still there is no enough water in the pore,
>>the water
>>is moving away from the channel during step 4 &5?
>>
>>How can I solve this problem? Also how will I know how many water
>>molecules
>>will be sufficient for the channel?
>>
>>Thanks for your support.
>>
>>
>>-- gmx-users mailing listgmx-users@gromacs.org
>>
>>
>>http://lists.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 thewww
>>interface or send it to gmx-users-requ...@gromacs.org
>>.
>>
>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
>>
>> --
>> Aswathy
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/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
>



-- 
Aswathy
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Re: [gmx-users] Enough hydration of the channel

[Justin A. Lemkul]

Aswathy wrote:

Thank you very much.

In some papers I have seen the graph for hydration of the channel. How 
can we calculate that using Gromacs ? (or any other program?)


Have a look at some of Oliver Beckstein's programs:

http://sbcb.bioch.ox.ac.uk/oliver/software/

There are several that might be useful to you.

-Justin



Regards,
-Aswathy


On Thu, Jun 17, 2010 at 7:52 PM, > wrote:


Determining how many waters is sufficient is a tough problem, try
successive runs of option #3, below. As for the simpler topic of
getting more hydration:

1. If the issue is simply getting the channel hydrated enough to
overcome some transition from dry to wet, then run a neat water box
od 216 spc for 100 ps and extract a frame every 10 ps, then run
genbox 10x successively using each of these frames. This should give
you massive hydration.

2. If that doesn't work, then you could add a new equilibration step
where you posres some cap waters so that the channel can not dry
out. This may allow SC's to equilibrate to a wet environment.

3. If the issue is that the water is still moving out, then why not
do SMD on a water into the pore and find out where the repulsion is.

-- original message --

Hi everyone,

I have a homology model of a transporter. I want to study the ligand
transport through the channel. i have done the following steps.

1. Ligand has docked to the mouth of the channel
2.  Inserted the complex in POPC bilayer, then solvated, and
equilibrated
for 4ns(with position restarint on Protein & ligand)
3. Then I saw tht there are very few wtaer inside the pore, Since this
channel is an aqueous pore, I have added water to the channel using
genbox.
4. Then the complete system equilibrated for pico seconds.
5,in order to select different snap shots for SMD (want to do a multiple
SMDs with different starting structures.) I have run 1ns Production
run and
selected different frames.

Suddenly I found that still there is no enough water in the pore,
the water
is moving away from the channel during step 4 &5?

How can I solve this problem? Also how will I know how many water
molecules
will be sufficient for the channel?

Thanks for your support.


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


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Please search the archive at http://www.gromacs.org/search before
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.
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--
Aswathy



--


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


--
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Re: [gmx-users] Enough hydration of the channel

[Aswathy]

Thank you very much.

In some papers I have seen the graph for hydration of the channel. How can
we calculate that using Gromacs ? (or any other program?)

Regards,
-Aswathy


On Thu, Jun 17, 2010 at 7:52 PM,  wrote:

> Determining how many waters is sufficient is a tough problem, try
> successive runs of option #3, below. As for the simpler topic of getting
> more hydration:
>
> 1. If the issue is simply getting the channel hydrated enough to overcome
> some transition from dry to wet, then run a neat water box od 216 spc for
> 100 ps and extract a frame every 10 ps, then run genbox 10x successively
> using each of these frames. This should give you massive hydration.
>
> 2. If that doesn't work, then you could add a new equilibration step where
> you posres some cap waters so that the channel can not dry out. This may
> allow SC's to equilibrate to a wet environment.
>
> 3. If the issue is that the water is still moving out, then why not do SMD
> on a water into the pore and find out where the repulsion is.
>
> -- original message --
>
> Hi everyone,
>
> I have a homology model of a transporter. I want to study the ligand
> transport through the channel. i have done the following steps.
>
> 1. Ligand has docked to the mouth of the channel
> 2.  Inserted the complex in POPC bilayer, then solvated, and equilibrated
> for 4ns(with position restarint on Protein & ligand)
> 3. Then I saw tht there are very few wtaer inside the pore, Since this
> channel is an aqueous pore, I have added water to the channel using genbox.
> 4. Then the complete system equilibrated for pico seconds.
> 5,in order to select different snap shots for SMD (want to do a multiple
> SMDs with different starting structures.) I have run 1ns Production run and
> selected different frames.
>
> Suddenly I found that still there is no enough water in the pore, the water
> is moving away from the channel during step 4 &5?
>
> How can I solve this problem? Also how will I know how many water molecules
> will be sufficient for the channel?
>
> Thanks for your support.
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.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 thewww interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



-- 
Aswathy
-- 
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Re: [gmx-users] git

[Justin A. Lemkul]

Sai Pooja wrote:

Hi,
 
This is the first time I am using git. I tried to get started by using 
- git clone git://git.gromacs.org/gromacs.git 
 - command but got an error - 
"command not found: git" (I have tried different versions of this 
command available with the same result). I am sure this is something 
extremely trivial. Can someone let me know what am I doing wrong? 
 


Have you actually installed git?  If so, it may just not be in your $PATH.  If 
not, install it before you try to use it :)


-Justin


Regards
Pooja
 



--
Quaerendo Invenietis-Seek and you shall discover.



--


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


--
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[gmx-users] git

[Sai Pooja]

Hi,

This is the first time I am using git. I tried to get started by using - git
clone git://git.gromacs.org/gromacs.git - command but got an error -
"command not found: git" (I have tried different versions of this command
available with the same result). I am sure this is something extremely
trivial. Can someone let me know what am I doing wrong?

Regards
Pooja



-- 
Quaerendo Invenietis-Seek and you shall discover.
-- 
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Re: [gmx-users] constraints bond length vari by 10%

[Mark Abraham]

- Original Message -
From: Sebastian Waltz 
Date: Thursday, June 17, 2010 18:59
Subject: Re: [gmx-users] constraints bond length vari by 10%
To: Discussion list for GROMACS users 

> Hi,
> 
> I did read the Documentation 5 times now, but I still not
> get is what the shake_tol does tell me. I tried it with 10
> values and can't figure out what it does. My CO bonds are
> constraint. Otherwise I would have bigger variations of the
> bond length. My .mdp file looks like this
> 
> constraints = none
> constraint_algorithm= shake
> shake_tol   = 0.05
> unconstrained_start = no
> 
> My question is more how I can constrain the bond length
> such that they vary only by a factor of +/- 0.0001. 

The above is fine, except that your topology probably has no constraints 
defined in it, because your [constraints] is in the wrong place. Try commenting 
out the contents of your constraints directive and see if you get identical 
results. This is the last time I'm going to repeat myself, since you're 
appearing to ignore my feedback :-)

Mark

> On Thu, 17 Jun 2010 08:01:04 +1000
>  Mark Abraham  wrote:
> > 
> > 
> > - Original Message -
> > From: Sebastian Waltz
> > 
> > Date: Thursday, June 17, 2010 2:23
> > Subject: Re: [gmx-users] constraints bond length vari by
> > 10%
> > To: Discussion list for GROMACS users
> > 
> > 
> > > Hi Mark,
> > > 
> > > what I have written in the .top you can see in my first
> > > massage. 
> > 
> > OK - but my suggestion was that it was put in the wrong
> > *place* and I don't have enough information to say
> > whether that's true.
> > 
> > > I actually don't know what to write what and in
> > > which .itp/.tpr file I have to add something and I also
> > > can't find something in the Internet. The documentation
> > for
> > > the constraints is just bad.
> > 
> > I understand your frustration, but documentation can't
> > anticipate the answer to every question or it would be
> > infinitely long. That fact doesn't make it bad. What the
> > documentation can do is provide general instruction. If
> > my guess is correct, then the worked example of a .top
> > file in Chapter 5 will help you understand where
> > [constraints] needs to go. Specifically, page 109 will
> > point out that
> > 
> > #include "ffforcefield.itp"
> > [ moleculetype ]
> > ...
> > [atoms]
> > ...
> > 
> > #include "water.itp"
> > 
> > [system]
> > ...
> > [molecules]
> > ...
> > 
> > [constraints]
> > ...
> > 
> > won't work.
> > 
> > Section 5.5 has a worked example of how to use [settles]
> > which are a kind of constraint, and work the same way.
> > 
> > Once you've worked through this information, if you still
> > have a problem with the documention, then a constructive
> > suggestion for improvement would be welcome :-)
> > 
> > Mark
> > 
> > > On Wed, 16 Jun 2010 09:05:20 +1000
> > >  Mark Abraham  wrote:
> > > > 
> > > > 
> > > > - Original Message -
> > > > From: Sebastian Waltz
> > > > 
> > > > Date: Tuesday, June 15, 2010 22:09
> > > > Subject: [gmx-users] constraints bond length vari by
> > 10%
> > > > To: gmx-users@gromacs.org
> > > > 
> > > > > Hi all,
> > > > > 
> > > > > I added constraints on some bonds in my system by
> > > > adding 
> > > > > 
> > > > > [ constraints ]
> > > > > ;ai   aj  typedistance
> > > > >40 41  1   0.1230
> > > > >47 48  1   0.1230
> > > > >54 55  1   0.1230
> > > > >61 62  1   0.1230
> > > > > 
> > > > > to me top file (CO double bonds) and in the mdp
> > file 
> > > > > 
> > > > > 
> constraints 
> > > > > =  none
> > > > > 
> > > > > . I thought this should more or less fix my bond
> > > > lengths.
> > > > > Nether the less the bond lengths vary by 10%. Did I
> > > > make
> > > > > something or is it quite normal? What would be the
> > way
> > > > to
> > > > > fix the bond length so that they vary only by ca.
> > 1%.
> > > > 
> > > > You're using the right approach, but you've probably
> > not
> > > > put your [constraints] directive in the right
> > > > [moleculetype], or used the wrong .top/.itp/.tpr file
> > at
> > > > some point.
> > > > 
> > > > Mark
> > > > 
> > > 
> > > -- 
> > > gmx-users mailing listgmx-users@gromacs.org
> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > Please search the archive at
> > http://www.gromacs.org/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
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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> before posting!
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Re: [gmx-users] Incomplete ring

[David van der Spoel]

On 2010-06-17 21.06, you zou wrote:

Hi Users,

I have a .pdb file, in this file when I want to use pdb2gmx command
there is this error massage:
Fatal error:
Incomplete ring in HIS680

this aminoacid is not complete in general, I don't know how can I
complete this such that I don't add HIS for complete? Please give me a hint.


add the missing atoms with emacs (or another text editor). Then minimize.

Thank you


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[gmx-users] Incomplete ring

[you zou]

Hi Users,
I have a .pdb file, in this file when I want to use pdb2gmx command there is 
this error massage:Fatal error:Incomplete ring in HIS680
this aminoacid is not complete in general, I don't know how can I complete this 
such that I don't add HIS for complete? Please give me a hint.
Thank you 
_
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Re: [gmx-users] [pairs] and [dihedrals]

[Justin A. Lemkul]

you zou wrote:

Hi everyone,

I have one question about topology, If I want to write topology by hand, 
how can I write pairs and dihedrals without mistakes? Is there any free 
softwares to use?




If you're using some automated program, then you're not doing it by hand :) 
There are several on the Gromacs' User Contribution site.  There is no 
substitute for understanding the intrinsics of your desired force field and how 
it treats these terms, as well as Chapter 5 of the Gromacs manual. 
Understanding all of this is the only way to not make mistakes (being careful of 
course to properly implement all that you have learned from your reading).


-Justin


Thank you


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


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[gmx-users] [pairs] and [dihedrals]

[you zou]

Hi everyone,
I have one question about topology, If I want to write topology by hand, how 
can I write pairs and dihedrals without mistakes? Is there any free softwares 
to use?
Thank you 
_
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Re: [gmx-users] large forces and monstrous water molecules in energy minimization step

[Ran Friedman]

Hi,

For the dynamics to work you indeed need smaller forces (on the order of
10^3 in GMX units).
Using flexible water molecules I was able to get this for your NaCl model. 
Just add:
define  =  -DFLEXIBLE
To your input.

This should work also to fill in the voids I guess.

Ran

-- 
--
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Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-639
Email: r.fried...@bioc.uzh.ch
Skype: ran.friedman
--

Justin A. Lemkul wrote:
>
> Use a different box size.  I replicated your problem, but your run
> completes successfully with a box set up with editconf -d 1 instead of
> -d 3.3.
>
> If you set nstxout = 1 during the EM process, you'll see the
> problematic water molecule become unstable.  It looks as if there is a
> small void in the solvent (due to the way genbox tries to stack
> solvent configurations) and your water molecule simply can't find a
> good orientation within that void.
>
> -Justin
>
> Ehud Schreiber wrote:
>> Dear GROMACS users,
>>
>>  
>>
>> When trying to simulate a pair of interacting proteins in water, I
>> have encountered problems that ultimately resulted in the simulation
>> crashing. I then tried to simplify the system as far as possible
>> while retaining the problem; I now believe the problem (or at least a
>> part of it) lies in the energy minimization step (the first molecular
>> dynamics one). Specifically, the forces encountered during this step
>> are very large, and some water molecules (which are supposed to be
>> rigid) become giant and misshapen.
>>
>>  
>>
>> In more details:
>>
>> 1) I use GROMACS version 4.0.7, single precision, on a server with
>> two Intel x86-64 processors and the redhat 5.4 linux OS.
>>
>> 2) I created a PDB file, called NaCl.pdb, with only two “atoms”,
>> actually Na+ and Cl- ions separated by their distance in the lattice
>> of salt:
>>
>>  
>>
>> HET NA  A   1   1
>>
>> HET CL  A   1   1
>>
>> HETNAM  NA SODIUM ION
>>
>> HETNAM  CL CHLORIDE ION
>>
>> FORMUL   1   NANA 1+
>>
>> FORMUL   2   CLCL 1-
>>
>> HETATM1 NANA A   1  -1.410.0   0.01.00 
>> 0.0  NA
>>
>> HETATM2 CLCL A   1  +1.410.0   0.01.00 
>> 0.0  CL
>>
>>  
>>
>> 3) I use the tip3p water model:
>>
>>  
>>
>> pdb2gmx -f NaCl.pdb -water tip3p
>>
>>  
>>
>> 4) I create the box:
>>
>>  
>>
>> editconf -f conf.gro -bt dodecahedron -d 3.3 -o box.gro
>>
>>  
>>
>> 5) I add water using spc216, creating the saltwater.gro file (which
>> seems O.K. by inspection):
>>
>>  
>>
>> genbox -cp box.gro -cs spc216.gro -p topol.top -o saltwater.gro
>>
>>  
>>
>> 6) I create the energy minimization parameter file em.mdp:
>>
>>  
>>
>> --em.mdp--
>>
>> integrator  = steep
>>
>> nsteps  = 200
>>
>> nstlist = 10
>>
>> rlist   = 1.0
>>
>> coulombtype = pme
>>
>> rcoulomb= 1.0
>>
>> vdwtype = Cut-off
>>
>> rvdw= 1.0
>>
>> nstenergy   = 10
>>
>> --
>>
>>  
>>
>> 7) I prepare the em.tpr file for the energy minimization run:
>>
>>  
>>
>> grompp -f em.mdp -p topol.top -c saltwater.gro -o em.tpr
>>
>>  
>>
>> 8) I run the energy minimization step:
>>
>>  
>>
>> mdrun -v -deffnm em
>>
>>  
>>
>> 9) Looking at the em.log file I see that this step converged to
>> machine precision but did not have maximal force < 10:
>>
>>  
>>
>> …
>>
>> Enabling SPC water optimization for 7561 molecules.
>>
>> …
>>
>> Max number of connections per atom is 2
>>
>> Total number of connections is 30244
>>
>> Max number of graph edges per atom is 2
>>
>> Total number of graph edges is 30244
>>
>> Going to use C-settle (7561 waters)
>>
>> wo = 0.33, wh =0.33, wohh = 3, rc = 0.075695, ra = 0.0390588
>>
>> rb = 0.0195294, rc2 = 0.15139, rone = 1, dHH = 0.15139, dOH = 0.09572
>>
>> …
>>
>> Stepsize too small, or no change in energy.
>>
>> Converged to machine precision,
>>
>> but not to the requested precision Fmax < 10
>>
>> …
>>
>> Steepest Descents converged to machine precision in 36 steps,
>>
>> but did not reach the requested Fmax < 10.
>>
>> Potential Energy  = -3.4678925e+05
>>
>> Maximum force =  6.4623531e+05 on atom 11052
>>
>> Norm of force =  5.4643726e+03
>>
>>  
>>
>> 10) Looking at the em.gro file I see one monstrous water molecule
>> (no. 3686); e.g., it has |HW2-OW| = 3.384876 nm, while the normal
>> distance is about 0.1 nm. Its HW2 atom (no. 11054) is close to
>> another water molecule (no. 5849), e.g., 0.047 nm from the latter’s
>> HW2 atom (no. 17543):
>>
>>  
>>
>> …
>>
>> 3686SOL OW11052   4.348   3.778  -0.629
>>
>> 3686SOLHW111053   5.360   2.601   0.505
>>
>> 3686SOLHW211054   6.518   1.650   0.861 
>> …
>>
>> 5849SOL OW17541   6.525   1.698   0.900
>>
>> 5849

[gmx-users] Enough hydration of the channel

[chris . neale]

Determining how many waters is sufficient is a tough problem, try  
successive runs of option #3, below. As for the simpler topic of  
getting more hydration:


1. If the issue is simply getting the channel hydrated enough to  
overcome some transition from dry to wet, then run a neat water box od  
216 spc for 100 ps and extract a frame every 10 ps, then run genbox  
10x successively using each of these frames. This should give you  
massive hydration.


2. If that doesn't work, then you could add a new equilibration step  
where you posres some cap waters so that the channel can not dry out.  
This may allow SC's to equilibrate to a wet environment.


3. If the issue is that the water is still moving out, then why not do  
SMD on a water into the pore and find out where the repulsion is.


-- original message --

Hi everyone,

I have a homology model of a transporter. I want to study the ligand
transport through the channel. i have done the following steps.

1. Ligand has docked to the mouth of the channel
2.  Inserted the complex in POPC bilayer, then solvated, and equilibrated
for 4ns(with position restarint on Protein & ligand)
3. Then I saw tht there are very few wtaer inside the pore, Since this
channel is an aqueous pore, I have added water to the channel using genbox.
4. Then the complete system equilibrated for pico seconds.
5,in order to select different snap shots for SMD (want to do a multiple
SMDs with different starting structures.) I have run 1ns Production run and
selected different frames.

Suddenly I found that still there is no enough water in the pore, the water
is moving away from the channel during step 4 &5?

How can I solve this problem? Also how will I know how many water molecules
will be sufficient for the channel?

Thanks for your support.


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Re: [gmx-users] large forces and monstrous water molecules in energy minimization step

[Justin A. Lemkul]

Use a different box size.  I replicated your problem, but your run completes 
successfully with a box set up with editconf -d 1 instead of -d 3.3.


If you set nstxout = 1 during the EM process, you'll see the problematic water 
molecule become unstable.  It looks as if there is a small void in the solvent 
(due to the way genbox tries to stack solvent configurations) and your water 
molecule simply can't find a good orientation within that void.


-Justin

Ehud Schreiber wrote:

Dear GROMACS users,

 

When trying to simulate a pair of interacting proteins in water, I have 
encountered problems that ultimately resulted in the simulation 
crashing. I then tried to simplify the system as far as possible while 
retaining the problem; I now believe the problem (or at least a part of 
it) lies in the energy minimization step (the first molecular dynamics 
one). Specifically, the forces encountered during this step are very 
large, and some water molecules (which are supposed to be rigid) become 
giant and misshapen.


 


In more details:

1) I use GROMACS version 4.0.7, single precision, on a server with two 
Intel x86-64 processors and the redhat 5.4 linux OS.


2) I created a PDB file, called NaCl.pdb, with only two “atoms”, 
actually Na+ and Cl- ions separated by their distance in the lattice of 
salt:


 


HET NA  A   1   1

HET CL  A   1   1

HETNAM  NA SODIUM ION

HETNAM  CL CHLORIDE ION

FORMUL   1   NANA 1+

FORMUL   2   CLCL 1-

HETATM1 NANA A   1  -1.410.0   0.01.00  0.0  NA

HETATM2 CLCL A   1  +1.410.0   0.01.00  0.0  CL

 


3) I use the tip3p water model:

 


pdb2gmx -f NaCl.pdb -water tip3p

 


4) I create the box:

 


editconf -f conf.gro -bt dodecahedron -d 3.3 -o box.gro

 

5) I add water using spc216, creating the saltwater.gro file (which 
seems O.K. by inspection):


 


genbox -cp box.gro -cs spc216.gro -p topol.top -o saltwater.gro

 


6) I create the energy minimization parameter file em.mdp:

 


--em.mdp--

integrator  = steep

nsteps  = 200

nstlist = 10

rlist   = 1.0

coulombtype = pme

rcoulomb= 1.0

vdwtype = Cut-off

rvdw= 1.0

nstenergy   = 10

--

 


7) I prepare the em.tpr file for the energy minimization run:

 


grompp -f em.mdp -p topol.top -c saltwater.gro -o em.tpr

 


8) I run the energy minimization step:

 


mdrun -v -deffnm em

 

9) Looking at the em.log file I see that this step converged to machine 
precision but did not have maximal force < 10:


 


…

Enabling SPC water optimization for 7561 molecules.

…

Max number of connections per atom is 2

Total number of connections is 30244

Max number of graph edges per atom is 2

Total number of graph edges is 30244

Going to use C-settle (7561 waters)

wo = 0.33, wh =0.33, wohh = 3, rc = 0.075695, ra = 0.0390588

rb = 0.0195294, rc2 = 0.15139, rone = 1, dHH = 0.15139, dOH = 0.09572

…

Stepsize too small, or no change in energy.

Converged to machine precision,

but not to the requested precision Fmax < 10

…

Steepest Descents converged to machine precision in 36 steps,

but did not reach the requested Fmax < 10.

Potential Energy  = -3.4678925e+05

Maximum force =  6.4623531e+05 on atom 11052

Norm of force =  5.4643726e+03

 

10) Looking at the em.gro file I see one monstrous water molecule (no. 
3686); e.g., it has |HW2-OW| = 3.384876 nm, while the normal distance is 
about 0.1 nm. Its HW2 atom (no. 11054) is close to another water 
molecule (no. 5849), e.g., 0.047 nm from the latter’s HW2 atom (no. 17543):


 


…

3686SOL OW11052   4.348   3.778  -0.629

3686SOLHW111053   5.360   2.601   0.505

3686SOLHW211054   6.518   1.650   0.861  


…

5849SOL OW17541   6.525   1.698   0.900

5849SOLHW117542   6.606   1.649   0.918

5849SOLHW217543   6.481   1.648   0.832

…

 

11) During the simulation, several files called stepnnl.pdb were 
produced for problematic steps, where nn=11,15,19 and l=b,c. For 
example, the file step19c.pdb indeed shows a problematic water molecule 
no. 3686, while step19b.pdb does not. Likewise, the earlier step11c.pdb 
shows a problematic water molecule no. 3266 while step11b.pdb seems 
proper. The stdout/stderr of mdrun contains warnings like the following:


 


…

t = 0.019 ps: Water molecule starting at atom 11052 can not be settled.

Check for bad contacts and/or reduce the timestep.

…

 

12) Reducing the neighbor list update time, i.e., setting nstlist = 1, 
does not produce any change.


 

13) Trying to use the conjugate gradient integrator instead of steepest 
descent, i.e., setting integrator = cg, is even worse - the running crashes:


 


…

Step 16, Epot=-1.258771e+35, Fnorm=  nan, Fmax=  inf (atom 14493)

Segmentation fault

Exit 139

 

 

 


So, am I doing something wrong? How can I avoid these problems?

 


Thanks,

Ehud Schreiber.

 

[gmx-users] RE: Parallel instalation: gmx-users Digest, Vol 74, Issue 76

[abdul wadood]

Dear Carsten

I give the path for the topol.tpr file now the error is change which is

Fatal error:
3: Too many LINCS warnings (4254)
3: If you know what you are doing you can adjust the lincs warning threshold in 
your mdp file
3: or set the environment variable GMX_MAXCONSTRWARN to -1,
3: but normally it is better to fix the problem
3: ---
3:
3: "You're About to Hurt Somebody" (Jazzy Jeff)
3:
3: Halting program mdrun_mpi
3:
3: gcq#98: "You're About to Hurt Somebody" (Jazzy Jeff)
3:
3: [0] MPI Abort by user Aborting program !
3: [0] Aborting program!
3: p4_error: latest msg from perror: No such file or directory


Abdul Wadood, 
Research Scholar, 
Dr.Panjwani Center for Molecular Medicine and 
Drug Research, 
International Center for Chemical and 
Biological Science, 
University of Karachi, Karachi-75720, Pakistan. 
Email:wadoodbiochem...@hotmail.com 




Subject: Re: Parallel instalation:  gmx-users Digest, Vol 74, Issue 76
From: ckut...@gwdg.de
Date: Thu, 17 Jun 2010 15:46:40 +0200
CC: wadoodbiochem...@hotmail.com
To: gmx-users@gromacs.org



On Jun 17, 2010, at 3:42 PM, abdul wadood wrote:Dear Carsten 

the command which i give is 

mpiexec -l -np 4 /usr/local/gromacs/bin/mdrun_mpi -s topol.tpr

with this command the same error come which is 

Can not open file:
3: topol.tpr
3: ---
Maybe "." (the current directory) is not in your path. Either try
mpiexec -l -np 4 /usr/local/gromacs/bin/mdrun_mpi -s ./topol.tpr
or give the full path name:
mpiexec -l -np 4 /usr/local/gromacs/bin/mdrun_mpi -s  
/absolute/path/to/topol.tpr
Carsten


  
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[gmx-users] large forces and monstrous water molecules in energy minimization step

[Ehud Schreiber]

Dear GROMACS users,

 

When trying to simulate a pair of interacting proteins in water, I have
encountered problems that ultimately resulted in the simulation
crashing. I then tried to simplify the system as far as possible while
retaining the problem; I now believe the problem (or at least a part of
it) lies in the energy minimization step (the first molecular dynamics
one). Specifically, the forces encountered during this step are very
large, and some water molecules (which are supposed to be rigid) become
giant and misshapen.

 

In more details:

1) I use GROMACS version 4.0.7, single precision, on a server with two
Intel x86-64 processors and the redhat 5.4 linux OS.

2) I created a PDB file, called NaCl.pdb, with only two "atoms",
actually Na+ and Cl- ions separated by their distance in the lattice of
salt:

 

HET NA  A   1   1

HET CL  A   1   1

HETNAM  NA SODIUM ION

HETNAM  CL CHLORIDE ION 

FORMUL   1   NANA 1+

FORMUL   2   CLCL 1- 

HETATM1 NANA A   1  -1.410.0   0.01.00  0.0
NA

HETATM2 CLCL A   1  +1.410.0   0.01.00  0.0
CL 

 

3) I use the tip3p water model:

 

pdb2gmx -f NaCl.pdb -water tip3p

 

4) I create the box:

 

editconf -f conf.gro -bt dodecahedron -d 3.3 -o box.gro

 

5) I add water using spc216, creating the saltwater.gro file (which
seems O.K. by inspection):

 

genbox -cp box.gro -cs spc216.gro -p topol.top -o saltwater.gro

 

6) I create the energy minimization parameter file em.mdp:

 

--em.mdp--

integrator  = steep 

nsteps  = 200

nstlist = 10

rlist   = 1.0

coulombtype = pme

rcoulomb= 1.0

vdwtype = Cut-off

rvdw= 1.0

nstenergy   = 10

--

 

7) I prepare the em.tpr file for the energy minimization run:

 

grompp -f em.mdp -p topol.top -c saltwater.gro -o em.tpr

 

8) I run the energy minimization step:

 

mdrun -v -deffnm em

 

9) Looking at the em.log file I see that this step converged to machine
precision but did not have maximal force < 10:

 

...

Enabling SPC water optimization for 7561 molecules.

...

Max number of connections per atom is 2

Total number of connections is 30244

Max number of graph edges per atom is 2

Total number of graph edges is 30244

Going to use C-settle (7561 waters)

wo = 0.33, wh =0.33, wohh = 3, rc = 0.075695, ra = 0.0390588

rb = 0.0195294, rc2 = 0.15139, rone = 1, dHH = 0.15139, dOH = 0.09572

...

Stepsize too small, or no change in energy.

Converged to machine precision,

but not to the requested precision Fmax < 10

...

Steepest Descents converged to machine precision in 36 steps,

but did not reach the requested Fmax < 10.

Potential Energy  = -3.4678925e+05

Maximum force =  6.4623531e+05 on atom 11052

Norm of force =  5.4643726e+03

 

10) Looking at the em.gro file I see one monstrous water molecule (no.
3686); e.g., it has |HW2-OW| = 3.384876 nm, while the normal distance is
about 0.1 nm. Its HW2 atom (no. 11054) is close to another water
molecule (no. 5849), e.g., 0.047 nm from the latter's HW2 atom (no.
17543):

 

...

3686SOL OW11052   4.348   3.778  -0.629

3686SOLHW111053   5.360   2.601   0.505

3686SOLHW211054   6.518   1.650   0.861  

...

5849SOL OW17541   6.525   1.698   0.900

5849SOLHW117542   6.606   1.649   0.918

5849SOLHW217543   6.481   1.648   0.832

...

 

11) During the simulation, several files called stepnnl.pdb were
produced for problematic steps, where nn=11,15,19 and l=b,c. For
example, the file step19c.pdb indeed shows a problematic water molecule
no. 3686, while step19b.pdb does not. Likewise, the earlier step11c.pdb
shows a problematic water molecule no. 3266 while step11b.pdb seems
proper. The stdout/stderr of mdrun contains warnings like the following:

 

...

t = 0.019 ps: Water molecule starting at atom 11052 can not be settled.

Check for bad contacts and/or reduce the timestep.

...

 

12) Reducing the neighbor list update time, i.e., setting nstlist = 1,
does not produce any change.

 

13) Trying to use the conjugate gradient integrator instead of steepest
descent, i.e., setting integrator = cg, is even worse - the running
crashes:

 

...

Step 16, Epot=-1.258771e+35, Fnorm=  nan, Fmax=  inf (atom
14493)

Segmentation fault

Exit 139

 

 

 

So, am I doing something wrong? How can I avoid these problems?

 

Thanks,

Ehud Schreiber.

 

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[gmx-users] Enough hydration of the channel

[Aswathy]

Hi everyone,

I have a homology model of a transporter. I want to study the ligand
transport through the channel. i have done the following steps.

1. Ligand has docked to the mouth of the channel
2.  Inserted the complex in POPC bilayer, then solvated, and equilibrated
for 4ns(with position restarint on Protein & ligand)
3. Then I saw tht there are very few wtaer inside the pore, Since this
channel is an aqueous pore, I have added water to the channel using genbox.
4. Then the complete system equilibrated for pico seconds.
5,in order to select different snap shots for SMD (want to do a multiple
SMDs with different starting structures.) I have run 1ns Production run and
selected different frames.

Suddenly I found that still there is no enough water in the pore, the water
is moving away from the channel during step 4 &5?

How can I solve this problem? Also how will I know how many water molecules
will be sufficient for the channel?

Thanks for your support.

-- 
Aswathy
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[gmx-users] Re: Parallel instalation: gmx-users Digest, Vol 74, Issue 76

[Carsten Kutzner]

On Jun 17, 2010, at 3:42 PM, abdul wadood wrote:

> Dear Carsten 
> 
> the command which i give is 
> 
> mpiexec -l -np 4 /usr/local/gromacs/bin/mdrun_mpi -s topol.tpr
> 
> with this command the same error come which is 
> 
> Can not open file:
> 3: topol.tpr
> 3: ---
Maybe "." (the current directory) is not in your path. Either try

mpiexec -l -np 4 /usr/local/gromacs/bin/mdrun_mpi -s ./topol.tpr

or give the full path name:

mpiexec -l -np 4 /usr/local/gromacs/bin/mdrun_mpi -s  
/absolute/path/to/topol.tpr

Carsten



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Re: [gmx-users] System net charge

[Justin A. Lemkul]

Rabab Toubar wrote:

I have noticed that you get the overall charge WHILE you are setting up the 
system - when using grompp I think. Now if after the mdrun and I want to check 
the overall charge, how can I possibly do that?
I tried the mailing list but didn't find an answer to my question


The net charge of any molecule (if processed by pdb2gmx) is printed in the 
topology at the end of the [atoms] directive.  Otherwise, take note of what 
grompp tells you and/or log all your output.


-Justin



Thanks
Rabab Toubar



  



--


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


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[gmx-users] System net charge

[Rabab Toubar]

I have noticed that you get the overall charge WHILE you are setting up the 
system - when using grompp I think. Now if after the mdrun and I want to check 
the overall charge, how can I possibly do that?
I tried the mailing list but didn't find an answer to my question

Thanks
Rabab Toubar



  

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Re: [gmx-users] Re: His protonation

[Justin A. Lemkul]

Rabab Toubar wrote:

So is there a way we can make His neutral before running the simulations as in 
case of NAMD?


You can manually set any protonation state you want with pdb2gmx -his.

-Justin


Rabab Toubar



--- On Wed, 6/16/10, Justin A. Lemkul  wrote:


From: Justin A. Lemkul 
Subject: [gmx-users] Re: His protonation
To: "sagar barage" , "Gromacs Users' List" 

Date: Wednesday, June 16, 2010, 11:59 PM

Please keep all Gromacs-related correspondence on the
gmx-users list.  I am not a private tutor.

sagar barage wrote:

Dear sir,
 

   when i was done the MD of crystal
structure the both nitrogen of immadazol ring of histidine
is protonated

which are not protonated in crystal structure.

There are no protons in crystal structures.


  all histidine in

structure contain single protonation but some Histidine is
double protonated at both nitrogen

why this happens in gromacs?


Please read the manual information (or pdb2gmx -h) about
how pdb2gmx attempts to add hydrogens to the input
structure.

-Justingm


-- Sagar H. Barage
sagarbar...@gmail.com



-- 

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


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--


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


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Re: [gmx-users] Re: His protonation

[Rabab Toubar]

So is there a way we can make His neutral before running the simulations as in 
case of NAMD?
Rabab Toubar



--- On Wed, 6/16/10, Justin A. Lemkul  wrote:

> From: Justin A. Lemkul 
> Subject: [gmx-users] Re: His protonation
> To: "sagar barage" , "Gromacs Users' List" 
> 
> Date: Wednesday, June 16, 2010, 11:59 PM
> 
> Please keep all Gromacs-related correspondence on the
> gmx-users list.  I am not a private tutor.
> 
> sagar barage wrote:
> > Dear sir,
> >         
>    when i was done the MD of crystal
> structure the both nitrogen of immadazol ring of histidine
> is protonated
> > which are not protonated in crystal structure.
> 
> There are no protons in crystal structures.
> 
> >          all histidine in
> structure contain single protonation but some Histidine is
> double protonated at both nitrogen
> > why this happens in gromacs?
> > 
> 
> Please read the manual information (or pdb2gmx -h) about
> how pdb2gmx attempts to add hydrogens to the input
> structure.
> 
> -Justingm
> 
> > -- Sagar H. Barage
> > sagarbar...@gmail.com
> 
> 
> -- 
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
> -- gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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> the www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 




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[gmx-users] how to correct velocities in trajectory file

[Dmitri Dubov]

Dear gmx'ers,

I've done a long NVE simulation in vacuo. During this run I had to take care to 
diminish the total energy drift, so my choice was

comm_mode = None

Now, analysing a smaller subsystem (solute + shell of solvent) I want to 
exclude its COM movement. Sorry, I fail to find any instruction how to do it. 
Extracting the subset with

trjconv -f traj.trr -s -n my_index.ndx -o subset.trr -center 

centers the subsystem well. But as it can be checked with

g_traj -f subset.trr -s subset.tpb -n my_index.ndx -ov -ekt -ekr -com

the velocities in subset.trr remain unchanged.
Ideally I would like, first, to correct the atom velocities to zero COM 
velocity, and next to correct them to obtain zero angular momentum of my 
subsystem. Could anyone advise me how to correct properly the velocities in 
trr-file?

Thank you in advance,

-- 
Regards,
 Dmitri  mailto:ddu...@ngs.ru-- 
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Re: [gmx-users] constraints bond length vari by 10%

[Sebastian Waltz]

Hi,

I did read the Documentation 5 times now, but I still not
get is what the shake_tol does tell me. I tried it with 10
values and can't figure out what it does. My CO bonds are
constraint. Otherwise I would have bigger variations of the
bond length. My .mdp file looks like this

constraints = none
constraint_algorithm= shake
shake_tol   = 0.05
unconstrained_start = no

My question is more how I can constrain the bond length
such that they vary only by a factor of +/- 0.0001. 

Thanks  


On Thu, 17 Jun 2010 08:01:04 +1000
 Mark Abraham  wrote:
> 
> 
> - Original Message -
> From: Sebastian Waltz
> 
> Date: Thursday, June 17, 2010 2:23
> Subject: Re: [gmx-users] constraints bond length vari by
> 10%
> To: Discussion list for GROMACS users
> 
> 
> > Hi Mark,
> > 
> > what I have written in the .top you can see in my first
> > massage. 
> 
> OK - but my suggestion was that it was put in the wrong
> *place* and I don't have enough information to say
> whether that's true.
> 
> > I actually don't know what to write what and in
> > which .itp/.tpr file I have to add something and I also
> > can't find something in the Internet. The documentation
> for
> > the constraints is just bad.
> 
> I understand your frustration, but documentation can't
> anticipate the answer to every question or it would be
> infinitely long. That fact doesn't make it bad. What the
> documentation can do is provide general instruction. If
> my guess is correct, then the worked example of a .top
> file in Chapter 5 will help you understand where
> [constraints] needs to go. Specifically, page 109 will
> point out that
> 
> #include "ffforcefield.itp"
> [ moleculetype ]
> ...
> [atoms]
> ...
> 
> #include "water.itp"
> 
> [system]
> ...
> [molecules]
> ...
> 
> [constraints]
> ...
> 
> won't work.
> 
> Section 5.5 has a worked example of how to use [settles]
> which are a kind of constraint, and work the same way.
> 
> Once you've worked through this information, if you still
> have a problem with the documention, then a constructive
> suggestion for improvement would be welcome :-)
> 
> Mark
> 
> > On Wed, 16 Jun 2010 09:05:20 +1000
> >  Mark Abraham  wrote:
> > > 
> > > 
> > > - Original Message -
> > > From: Sebastian Waltz
> > > 
> > > Date: Tuesday, June 15, 2010 22:09
> > > Subject: [gmx-users] constraints bond length vari by
> 10%
> > > To: gmx-users@gromacs.org
> > > 
> > > > Hi all,
> > > > 
> > > > I added constraints on some bonds in my system by
> > > adding 
> > > > 
> > > > [ constraints ]
> > > > ;ai aj  typedistance
> > > >40   41  1   0.1230
> > > >47   48  1   0.1230
> > > >54   55  1   0.1230
> > > >61   62  1   0.1230
> > > > 
> > > > to me top file (CO double bonds) and in the mdp
> file 
> > > > 
> > > > constraints 
> > > > =  none
> > > > 
> > > > . I thought this should more or less fix my bond
> > > lengths.
> > > > Nether the less the bond lengths vary by 10%. Did I
> > > make
> > > > something or is it quite normal? What would be the
> way
> > > to
> > > > fix the bond length so that they vary only by ca.
> 1%.
> > > 
> > > You're using the right approach, but you've probably
> not
> > > put your [constraints] directive in the right
> > > [moleculetype], or used the wrong .top/.itp/.tpr file
> at
> > > some point.
> > > 
> > > Mark
> > > 
> > 
> > -- 
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> http://www.gromacs.org/search 
> > before posting!
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> Use the 
> > www interface or send it to
> gmx-users-requ...@gromacs.org.
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> http://www.gromacs.org/mailing_lists/users.php

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[gmx-users] calculate interfacial tension

[kecy_wu]

Hello, I want to calculate the interfacial tension of the oil/water interface . 
I use 2D periodic boundary along Z axis , 
I get the interfacial teision from the .edr file (namely #Surf*SurfTen), 
it seems that the Surf*SurfTen is the total tension
 of the two interface ,is it that ?  Does it has any influence for I 
use the 2D periodic boundary along Z axis ?
 
Waiting for your  reply eagerly.
 
Thank you !
 
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Re: [gmx-users] Electric field, potential, dielectric constant

[Ran Friedman]

Hi,
You may want to use a Poisson-Boltzmann solver, e.g., APBS for this purpose.
Ran

Vladimir Lankevich wrote:
> Dear Gromacs Users,
>
> I have several questions about electrostatics in Gromacs.
> I am simulating two proteins in water, separated by certain distance,
> and was interested in their electrostatic interactions.
>
> I was wondering if Gromacs can calculate and show me values of
> electric field or electric potential at any point within the volume.
> If yes, how can this be done?
>
> I looked through the manual and did not find much. I tried using
> g_potential, but it only gives me ten values for electric field (if I
> use 10 slices, and particular direction).
> This confused me, because I thought that in the system each coordinate
> would have different electric field.
> How should I interpret the results of g_potential?
>
> Also, can I use Gromacs to compute dielectric constant of a particular
> region within the volume? How can I do that?
>
> Thank you very much!!
>
> Cheers,
> Vladimir

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Re: Subject: [gmx-users] error compiling mopac and gromacs

[subarna thakur]

According to the suggestion I have installed the f2c package in my machine.I am 
unable to find the g2c package. I have included the f2c library by - export 
LIBS="-lmopac -lf2c". But when I running  ./configure --with-qmmm-mopac 
--disable-float , an error is comming C compiler cannot create executable. The 
config.log file shows the following section- 
onfigure:3413: checking for C compiler default output file name
configure:3440: cc -I/usr/local/include -DUSE_MOPAC -L/usr/local/lib conftest.c 
-lmopac -lf2c >&5
/usr/lib/gcc/i486-linux-gnu/4.3.3/../../../../lib/libf2c.so: undefined 
reference to `MAIN__'
collect2: ld returned 1 exit status
configure:3443: $? = 1
configure:3481: result:
configure: failed program was:
| /* confdefs.h. */ 
Please suggest a way out.Subarna Thakur






From: Gerrit Groenhof 
To: gmx-users@gromacs.org
Sent: Sat, 12 June, 2010 3:36:54 PM
Subject: Re: Subject: [gmx-users] error compiling mopac and gromacs



Depending on how your libmopac.a was biuld, you need the to include the f2c or 
g2c library as well.

Gerrit



> Message: 5
> Date: Sat, 12 Jun 2010 14:33:02 +0530 (IST)
> From: subarna thakur 
> Subject: [gmx-users] error compiling  mopac and gromacs
> To: gmx-users@gromacs.org
> Message-ID: <371899.78968...@web95516.mail.in.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Hi 
> I am trying to link mopac with gromacs in a 32 bit linux machine. I have 
> downloaded the libmopac.a file and kept it under /usr/local/lib. I installed 
> fftw with double precision and then I set the enviornmental variables for 
> linking mopac and gromacs 
> export LDFLAGS="-L/usr/local/lib  -Wl,--wrap,__ctype_b"
> export CPPFLAGS="/usr/local/include -DUSE_MOPAC"
> export LIBS="lmopac
> 
> then I have ran the ./configure --with-qmmm-mopac --disable-float.It seems to 
> run ok.Then I used the make command but an error is comming as follows-
> /usr/local/lib/libmopac.a(lread.o)(.text+0x160): In function `e_rsle':
> : undefined reference to `__wrap___ctype_b'
> /usr/local/lib/libmopac.a(lread.o)(.text+0x21f): In function `e_rsle':
> : undefined reference to `__wrap___ctype_b'
> /usr/local/lib/libmopac.a(lread.o)(.text+0x296): In function `e_rsle':
> : undefined reference to `__wrap___ctype_b'
> /usr/local/lib/libmopac.a(lread.o)(.text+0x2d0): In function `e_rsle':
> : undefined reference to `__wrap___ctype_b'
> /usr/local/lib/libmopac.a(lread.o)(.text+0x8b2): In function `e_rsle':
> : undefined reference to `__wrap___ctype_b'
> /usr/local/lib/libmopac.a(lread.o)(.text+0xb05): more undefined references to 
> `__wrap___ctype_b' follow
> collect2: ld returned 1 exit status
> make[3]: *** [grompp] Error 1
> make[3]: Leaving directory `/usr/gromacs-4.0.3/src/kernel'
> make[2]: *** [all-recursive] Error 1
> make[2]: Leaving directory `/usr/gromacs-4.0.3/src'
> make[1]: *** [all] Error 2
> make[1]: Leaving directory `/usr/gromacs-4.0.3/src'
> make: *** [all-recursive] Error 1
>  
> Please suggest where I have gone wrong.
>  Subarna Thakur
> 
> 
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> End of gmx-users Digest, Vol 74, Issue 69
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--
Gerrit Groenhof
MPI biophysical chemistry
Goettingen
Germany
http://wwwuser.gwdg.de/~ggroenh/

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