[gmx-users] Re: change in secondary structure

[bharat gupta]

Hi,

I think I have asked this question earlier in the forum .. that during my
3ns simulation of a 230 amino acid proteins some portion of 2 beta strands
got converted to loop/random coil, after visualizing in VMD. I checked the
DSSP profile also .. and as per the DSSP results it's coil in that region ..
can anybody tell me where can the error be as I have been checking my
structure right from the minimization step till npt equilibration and its
was fine ... this has happened only after simulation ... pls help ??

-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com
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[gmx-users] Re:General MD question

[lloyd riggs]

Dear Carsten Kutzner,

First off, thanks.  I did not specify it in the input md.mdp file, but when I 
looked at the generated out.mdp it had a Linear center of mass removal for the 
groups [system].

When I added the pull vector it works, untill the two subunits crash(move past 
a realistic distance towards eachother and the force ==too much, and then it 
crashes after atoms fly offbut I get a change in dG up untill this point 
from solution.

I will try and play around today, but woundered if anyone could spot check my 
final .mdp input, as I lack in reviewers (for this portion of my work, ie 
people using gromacs).  As at some distant point in time I will try and publish 
dG/ dH and possibly dS, and relate these to affinities (Ka, KD and kD), I would 
like to make sure I did it correctly before the hellish number crunching(ie 
most time consuming) part.  I did look over the tutorial already...

Thanks

Stephan Watkins

Message: 3
Date: Tue, 1 Feb 2011 09:58:07 +0100
From: Carsten Kutzner 
Subject: Re: [gmx-users] General MD question
To: Discussion list for GROMACS users 
Message-ID: 
Content-Type: text/plain; charset=iso-8859-1

Hi Stephan,

On Jan 31, 2011, at 5:18 PM, lloyd riggs wrote:

> Dear All,
> 
> A quick question as I have not really delved into code for gromacs ever, nor 
> know anyone close whom has worked on it.
> 
> If I set up an MD simulation using a 4 protein complex, and 1 small peptide, 
> plus waters, etc...and run the whole thing the proteins never move, only the 
> amino acids within(constant temp RT and pressure 1 bar).
> 
> Two domains make one complex, and another two the other.  Basically, if I 
> seperate the domains say 5, 10, 15 angstrom, etc...the amino acids will drift 
> (the chains) towards each other, but the two large (global) protein units 
> never move their center (I know I can make it work with Pull vectors, but why 
> not in the simple system with a generated initial randomized velocities), I 
> woundered why they are fixed in a normal run with minimal parameters?  Is 
> there a reason (specific to developers), historical reason, or other?  As 
> waters move around fine, and anything else added (salt, small molecules of 
> 20-30 atoms, water) except the central molecule(s) of interest.
In a 'normal' run they should not be fixed. Could it be that you did 
accidentally
fix them by specifying center of mass removal (comm-grps in .mdp)?

Carsten

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Re: [gmx-users] Re: change in secondary structure

[Justin A. Lemkul]

bharat gupta wrote:

Hi,

I think I have asked this question earlier in the forum .. that during 
my 3ns simulation of a 230 amino acid proteins some portion of 2 beta 
strands got converted to loop/random coil, after visualizing in VMD. I 
checked the DSSP profile also .. and as per the DSSP results it's coil 
in that region .. can anybody tell me where can the error be as I have 
been checking my structure right from the minimization step till npt 
equilibration and its was fine ... this has happened only after 
simulation ... pls help ?? 



The comments I made last week still stand:

http://lists.gromacs.org/pipermail/gmx-users/2011-January/058014.html

You're basing your conclusions on a 3-ns simulation, which I would say is far 
too short to obtain any meaningful data for such a system.


-Justin


--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.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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Re: [gmx-users] Re: change in secondary structure

[bharat gupta]

Thanks for ur kind reply Justin ...

I also searched the gmx userlist regarding the same query and I found out
that It was mentioned to repeat the simulation again with a different force
field .. but I don't know about the energy minimization parameters as  I am
following ur lysozyme tutorial  for that .. I will get back to u get if I
get the same type of structural changes with this force field...

Also I would like to mention one more thing .. as I did the simulation of
crystal str of GFP with the same parameters which I used for the variant of
GFP .. In case of the crystal str. simulation result, it seems to be
perfectly fine and there is no change in the secondary structure also ...
So, if I am not wrong then there is some problem with the variant structure
that I have modeled ??.. Actually the variant of GFP that I have modeled has
one loop (of 4 amino acid in original str) replaced with an another loop of
9 residues length ... CAn this be the reason ??

Regarding the simulation time I want to ask ... what is the minimum or the
optimal time the structure should be simulated for such analysis as I have
read many paper published in big journals doing simulation only for 1ns (in
that case I am doing for 3 ns)... pls comment

On Wed, Feb 2, 2011 at 3:34 AM, Justin A. Lemkul  wrote:

>
>
> bharat gupta wrote:
>
>> Hi,
>>
>> I think I have asked this question earlier in the forum .. that during my
>> 3ns simulation of a 230 amino acid proteins some portion of 2 beta strands
>> got converted to loop/random coil, after visualizing in VMD. I checked the
>> DSSP profile also .. and as per the DSSP results it's coil in that region ..
>> can anybody tell me where can the error be as I have been checking my
>> structure right from the minimization step till npt equilibration and its
>> was fine ... this has happened only after simulation ... pls help ??
>>
>
> The comments I made last week still stand:
>
> http://lists.gromacs.org/pipermail/gmx-users/2011-January/058014.html
>
> You're basing your conclusions on a 3-ns simulation, which I would say is
> far too short to obtain any meaningful data for such a system.
>
> -Justin
>
>  --
>> Bharat
>> Ph.D. Candidate
>> Room No. : 7202A, 2nd Floor
>> Biomolecular Engineering Laboratory
>> Division of Chemical Engineering and Polymer Science
>> Pusan National University
>> Busan -609735
>> South Korea
>> Lab phone no. - +82-51-510-3680, +82-51-583-8343
>> Mobile no. - 010-5818-3680
>> E-mail : monu46...@yahoo.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 listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com
-- 
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[gmx-users] links warnangles

[vferrario]

Dear all,
I'm dealing with a simulation of a polymer in CHCL3, the polymer works  
good, but I have some problems with the CHCL3 definition in GROMOS  
53a6 ff.

I've taken the CHCL3 definition from the automated topology builder website:

http://compbio.biosci.uq.edu.au/atb/download.py?molid=1597&file=itp_uniatom

So the itp file of my CHCL3 definition is:

[ moleculetype ]
; Namenrexcl
CLF 3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass   
typeBchargeB  massB
 1CCL  1CLFCCl  1  0.179 12.011
; qtot 0.179
 2HCL  1CLFHCl  1  0.082  1.008
; qtot 0.261
 3   CLCL  1CLFCL1  1 -0.087 35.453
; qtot 0.174
 4   CLCL  1CLFCL2  1 -0.087 35.453
; qtot 0.087

 5   CLCL  1CLFCL3  1 -0.087 35.453   ; qtot 0

[ constraints ]
1 3 1 0.1758
1 4 1 0.1758
1 5 1 0.1758
2 3 1 0.233839
2 4 1 0.233839
2 5 1 0.233839
3 4 1 0.290283
3 5 1 0.290283
4 5 1 0.290283

I've generated a box of solvent, but when I try to minimize it with  
the following mdp file:


title   = Minimization
cpp = /lib/cpp
include = -I../top
constraints = none
integrator  = steep
emtol   = 2.5
emstep  = 0.01
nsteps  = 10
nbfgscorr   = 10
nstenergy   = 100
nstxtcout   = 0
xtc_grps= system
energygrps  = system
nstlist = 5
ns_type = grid
pbc = xyz
rlist   = 1.0
coulombtype = cut-off
rcoulomb= 1.0
vdwtype = cut-off
rvdw= 1.4
fourierspacing  = 0.15
fourier_nx  = 0
fourier_ny  = 0
fourier_nz  = 0
pme_order   = 4
optimize_fft= yes
tcoupl  = no
pcoupl  = no
gen_vel = no
constraint_algorithm= LINCS
lincs_order = 8
lincs_iter  = 2
nstlog  = 100
lincs_warnangle = 90

The system crash giving me the following error:

Fatal error:
Too many LINCS warnings (1413)
If you know what you are doing you can adjust the lincs warning  
threshold in your mdp file

or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem

My question is: why the system crash and why LINCS warnings are  
generated if all the molecule is constrained? What shell I do to avoid  
these probles? New CHCL3 definition?

Please help me, thank you in advance.

Valerio



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Re: [gmx-users] Re: change in secondary structure

[Justin A. Lemkul]

bharat gupta wrote:

Thanks for ur kind reply Justin ...

I also searched the gmx userlist regarding the same query and I found 
out that It was mentioned to repeat the simulation again with a 
different force field .. but I don't know about the energy minimization 
parameters as  I am following ur lysozyme tutorial  for that .. I will 
get back to u get if I get the same type of structural changes with this 
force field... 

Also I would like to mention one more thing .. as I did the simulation 
of crystal str of GFP with the same parameters which I used for the 
variant of GFP .. In case of the crystal str. simulation result, it 
seems to be perfectly fine and there is no change in the secondary 
structure also ... So, if I am not wrong then there is some problem with 
the variant structure that I have modeled ??.. Actually the variant of 
GFP that I have modeled has one loop (of 4 amino acid in original str) 
replaced with an another loop of 9 residues length ... CAn this be the 
reason ??




You cannot draw any sort of reliable conclusions from a single trajectory of 
such short length.


Regarding the simulation time I want to ask ... what is the minimum or 
the optimal time the structure should be simulated for such analysis as 
I have read many paper published in big journals doing simulation only 
for 1ns (in that case I am doing for 3 ns)... pls comment




There is no hard and fast rule for how long an MD simulation needs to be.  You 
need to collect sufficient data over a sufficient time period to model the 
behavior of interest, with the understanding of how long it should take for that 
certain phenomenon to occur.  Expectations also scale with the quality of the 
software and hardware.  The paper you linked before was from 1999, at which time 
the expectations of simulation length were exponentially shorter.  Most systems 
aren't even completely stable after only 1 ns of unrestrained MD.  Nowadays, 1 
ns can be completed in a matter of hours, so the expectation (by reviewers and 
journals) is that far more data can be collected such that you approach a 
biologically-relevant time scale.


For loop movement, 3 ns is at least 10 times too short, in my experience.  50 or 
100 ns would be more appropriate, but don't just take my word for it.  You 
should also conduct independent simulations (i.e., different starting velocities 
applied to the same structure) to run multiple simulations and do proper 
statistical analysis.  You wouldn't do one single assay at the bench, so why 
would you do one single simulation and expect it to be absolutely correct?  It 
is possible that a single simulation shows erroneous behavior and can be 
eliminated as an outlier with sufficient replicates and data analysis.


-Justin

On Wed, Feb 2, 2011 at 3:34 AM, Justin A. Lemkul > wrote:




bharat gupta wrote:

Hi,

I think I have asked this question earlier in the forum .. that
during my 3ns simulation of a 230 amino acid proteins some
portion of 2 beta strands got converted to loop/random coil,
after visualizing in VMD. I checked the DSSP profile also .. and
as per the DSSP results it's coil in that region .. can anybody
tell me where can the error be as I have been checking my
structure right from the minimization step till npt
equilibration and its was fine ... this has happened only after
simulation ... pls help ??


The comments I made last week still stand:

http://lists.gromacs.org/pipermail/gmx-users/2011-January/058014.html

You're basing your conclusions on a 3-ns simulation, which I would
say is far too short to obtain any meaningful data for such a system.

-Justin

-- 
Bharat

Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.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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Re: [gmx-users] links warnangles

[Justin A. Lemkul]

vferra...@units.it wrote:

Dear all,
I'm dealing with a simulation of a polymer in CHCL3, the polymer works 
good, but I have some problems with the CHCL3 definition in GROMOS 53a6 ff.
I've taken the CHCL3 definition from the automated topology builder 
website:


http://compbio.biosci.uq.edu.au/atb/download.py?molid=1597&file=itp_uniatom

So the itp file of my CHCL3 definition is:

[ moleculetype ]
; Namenrexcl
CLF 3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass  
typeBchargeB  massB
 1CCL  1CLFCCl  1  0.179 12.011   ; 
qtot 0.179
 2HCL  1CLFHCl  1  0.082  1.008   ; 
qtot 0.261
 3   CLCL  1CLFCL1  1 -0.087 35.453   ; 
qtot 0.174
 4   CLCL  1CLFCL2  1 -0.087 35.453   ; 
qtot 0.087
 5   CLCL  1CLFCL3  1 -0.087 35.453   ; 
qtot 0


[ constraints ]
1 3 1 0.1758
1 4 1 0.1758
1 5 1 0.1758
2 3 1 0.233839
2 4 1 0.233839
2 5 1 0.233839
3 4 1 0.290283
3 5 1 0.290283
4 5 1 0.290283

I've generated a box of solvent, but when I try to minimize it with the 
following mdp file:


title= Minimization
cpp= /lib/cpp
include= -I../top
constraints = none
integrator= steep
emtol= 2.5
emstep  = 0.01
nsteps= 10
nbfgscorr   = 10
nstenergy= 100
nstxtcout= 0
xtc_grps= system
energygrps= system
nstlist= 5


For EM, nstlist should be 1.


ns_type= grid
pbc = xyz
rlist= 1.0
coulombtype= cut-off


Plain cutoffs lead to bad artifacts and thus should generally not be used.


rcoulomb= 1.0
vdwtype = cut-off
rvdw= 1.4
fourierspacing= 0.15
fourier_nx  = 0
fourier_ny  = 0
fourier_nz  = 0
pme_order   = 4
optimize_fft= yes
tcoupl  = no
pcoupl  = no
gen_vel = no
constraint_algorithm= LINCS
lincs_order = 8
lincs_iter  = 2
nstlog  = 100
lincs_warnangle = 90

The system crash giving me the following error:

Fatal error:
Too many LINCS warnings (1413)
If you know what you are doing you can adjust the lincs warning 
threshold in your mdp file

or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem

My question is: why the system crash and why LINCS warnings are 
generated if all the molecule is constrained? What shell I do to avoid 
these probles? New CHCL3 definition?


The charges and atom types match exactly what the force field prescribes, so 
those are probably solid.


You need to simplify the problem.  You built a box, but it is failing.  Does an 
EM of a single molecule work, or does it fail as well?  Consult the following:


http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

-Justin


Please help me, thank you in advance.

Valerio



This message was sent using IMP, the Internet Messaging Program.




--


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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Please search the archive at 
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Re: [gmx-users] Re: change in secondary structure

[bharat gupta]

Thanks for such a detailed reply to my queries .. But conducting a 50ns
simulation will take time ... so i want to conduct independent simulation
and for that I searched some threads but was not able to get the proper
description and method... if u can guide me through an appropriate link ..
it would be much more helpful ..

On Wed, Feb 2, 2011 at 5:10 AM, Justin A. Lemkul  wrote:

>
>
> bharat gupta wrote:
>
>> Thanks for ur kind reply Justin ...
>>
>> I also searched the gmx userlist regarding the same query and I found out
>> that It was mentioned to repeat the simulation again with a different force
>> field .. but I don't know about the energy minimization parameters as  I am
>> following ur lysozyme tutorial  for that .. I will get back to u get if I
>> get the same type of structural changes with this force field...
>> Also I would like to mention one more thing .. as I did the simulation of
>> crystal str of GFP with the same parameters which I used for the variant of
>> GFP .. In case of the crystal str. simulation result, it seems to be
>> perfectly fine and there is no change in the secondary structure also ...
>> So, if I am not wrong then there is some problem with the variant structure
>> that I have modeled ??.. Actually the variant of GFP that I have modeled has
>> one loop (of 4 amino acid in original str) replaced with an another loop of
>> 9 residues length ... CAn this be the reason ??
>>
>>
> You cannot draw any sort of reliable conclusions from a single trajectory
> of such short length.
>
>
>  Regarding the simulation time I want to ask ... what is the minimum or the
>> optimal time the structure should be simulated for such analysis as I have
>> read many paper published in big journals doing simulation only for 1ns (in
>> that case I am doing for 3 ns)... pls comment
>>
>>
> There is no hard and fast rule for how long an MD simulation needs to be.
>  You need to collect sufficient data over a sufficient time period to model
> the behavior of interest, with the understanding of how long it should take
> for that certain phenomenon to occur.  Expectations also scale with the
> quality of the software and hardware.  The paper you linked before was from
> 1999, at which time the expectations of simulation length were exponentially
> shorter.  Most systems aren't even completely stable after only 1 ns of
> unrestrained MD.  Nowadays, 1 ns can be completed in a matter of hours, so
> the expectation (by reviewers and journals) is that far more data can be
> collected such that you approach a biologically-relevant time scale.
>
> For loop movement, 3 ns is at least 10 times too short, in my experience.
>  50 or 100 ns would be more appropriate, but don't just take my word for it.
>  You should also conduct independent simulations (i.e., different starting
> velocities applied to the same structure) to run multiple simulations and do
> proper statistical analysis.  You wouldn't do one single assay at the bench,
> so why would you do one single simulation and expect it to be absolutely
> correct?  It is possible that a single simulation shows erroneous behavior
> and can be eliminated as an outlier with sufficient replicates and data
> analysis.
>
> -Justin
>
>  On Wed, Feb 2, 2011 at 3:34 AM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>bharat gupta wrote:
>>
>>Hi,
>>
>>I think I have asked this question earlier in the forum .. that
>>during my 3ns simulation of a 230 amino acid proteins some
>>portion of 2 beta strands got converted to loop/random coil,
>>after visualizing in VMD. I checked the DSSP profile also .. and
>>as per the DSSP results it's coil in that region .. can anybody
>>tell me where can the error be as I have been checking my
>>structure right from the minimization step till npt
>>equilibration and its was fine ... this has happened only after
>>simulation ... pls help ??
>>
>>
>>The comments I made last week still stand:
>>
>>http://lists.gromacs.org/pipermail/gmx-users/2011-January/058014.html
>>
>>You're basing your conclusions on a 3-ns simulation, which I would
>>say is far too short to obtain any meaningful data for such a system.
>>
>>-Justin
>>
>>-- Bharat
>>Ph.D. Candidate
>>Room No. : 7202A, 2nd Floor
>>Biomolecular Engineering Laboratory
>>Division of Chemical Engineering and Polymer Science
>>Pusan National University
>>Busan -609735
>>South Korea
>>Lab phone no. - +82-51-510-3680, +82-51-583-8343
>>Mobile no. - 010-5818-3680
>>E-mail : monu46...@yahoo.com 
>>>
>>
>>
>>
>>-- 
>>
>>Justin A. Lemkul
>>Ph.D. Candidate
>>ICTAS Doctoral Scholar
>>MILES-IGERT Trainee
>>Department of Biochemistry
>>Vi

Re: [gmx-users] Re:General MD question

[Carsten Kutzner]

On Feb 2, 2011, at 11:48 AM, lloyd riggs wrote:

> Dear Carsten Kutzner,
> 
> First off, thanks.  I did not specify it in the input md.mdp file, but when I 
> looked at the generated out.mdp it had a Linear center of mass removal for 
> the groups [system].
> 
> When I added the pull vector it works, untill the two subunits crash(move 
> past a realistic distance towards eachother and the force ==too much, and 
> then it crashes after atoms fly offbut I get a change in dG up untill 
> this point from solution.
> 
> I will try and play around today, but woundered if anyone could spot check my 
> final .mdp input, as I lack in reviewers (for this portion of
I or somebody else can take a quick look for any obvious issues, but
nobody can guarantee the correctness of what you get, of course.
This is entirely your responsibility.

Carsten

> my work, ie people using gromacs).  As at some distant point in time I will 
> try and publish dG/ dH and possibly dS, and relate these to affinities (Ka, 
> KD and kD), I would like to make sure I did it correctly before the hellish 
> number crunching(ie most time consuming) part.  I did look over the tutorial 
> already...
> 
> Thanks
> 
> Stephan Watkins
> 
> Message: 3
> Date: Tue, 1 Feb 2011 09:58:07 +0100
> From: Carsten Kutzner 
> Subject: Re: [gmx-users] General MD question
> To: Discussion list for GROMACS users 
> Message-ID: 
> Content-Type: text/plain; charset=iso-8859-1
> 
> Hi Stephan,
> 
> On Jan 31, 2011, at 5:18 PM, lloyd riggs wrote:
> 
>> Dear All,
>> 
>> A quick question as I have not really delved into code for gromacs ever, nor 
>> know anyone close whom has worked on it.
>> 
>> If I set up an MD simulation using a 4 protein complex, and 1 small peptide, 
>> plus waters, etc...and run the whole thing the proteins never move, only the 
>> amino acids within(constant temp RT and pressure 1 bar).
>> 
>> Two domains make one complex, and another two the other.  Basically, if I 
>> seperate the domains say 5, 10, 15 angstrom, etc...the amino acids will 
>> drift (the chains) towards each other, but the two large (global) protein 
>> units never move their center (I know I can make it work with Pull vectors, 
>> but why not in the simple system with a generated initial randomized 
>> velocities), I woundered why they are fixed in a normal run with minimal 
>> parameters?  Is there a reason (specific to developers), historical reason, 
>> or other?  As waters move around fine, and anything else added (salt, small 
>> molecules of 20-30 atoms, water) except the central molecule(s) of interest.
> In a 'normal' run they should not be fixed. Could it be that you did 
> accidentally
> fix them by specifying center of mass removal (comm-grps in .mdp)?
> 
> Carsten
> 
> -- 
> GMX DSL Doppel-Flat ab 19,99 Euro/mtl.! Jetzt mit 
> gratis Handy-Flat! http://portal.gmx.net/de/go/dsl
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne




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Re: [gmx-users] Re: change in secondary structure

[Justin A. Lemkul]

bharat gupta wrote:
Thanks for such a detailed reply to my queries .. But conducting a 50ns 
simulation will take time ... so i want to conduct independent 
simulation and for that I searched some threads but was not able to get 
the proper description and method... if u can guide me through an 
appropriate link .. it would be much more helpful .. 



Each simulation begins with the assignment of random velocities (gen_vel = yes). 
 Specify different values of gen_seed (or leave it set to -1) to get different 
velocities each time.


-Justin

--


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] links warnangles

[vferrario]

I've just tried with a single CHCL3 molecule, here's the output:

Back Off! I just backed up md.log to ./#md.log.2#
Getting Loaded...
Reading file clfmin.tpr, VERSION 4.0.7 (single precision)
Loaded with Money

NNODES=2, MYRANK=1, HOSTNAME=biohazard
NODEID=1 argc=6
Making 1D domain decomposition 2 x 1 x 1

Step -1, time -0.001 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 301.323604, max 324.810791 (between atoms 1 and 3)
bonds that rotated more than 90 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Back Off! I just backed up step-1b_n1.pdb to ./#step-1b_n1.pdb.2#

Back Off! I just backed up step-1c_n1.pdb to ./#step-1c_n1.pdb.2#
Wrote pdb files with previous and current coordinates

Back Off! I just backed up traj.trr to ./#traj.trr.1#

Back Off! I just backed up ener.edr to ./#ener.edr.2#
Steepest Descents:
   Tolerance (Fmax)   =  2.5e+00
   Number of steps=   10
Step=0, Dmax= 1.0e-02 nm, Epot=  0.0e+00 Fmax= 0.0e+00, atom= 0

writing lowest energy coordinates.

Back Off! I just backed up clfmin.gro to ./#clfmin.gro.1#

Steepest Descents converged to Fmax < 2.5 in 1 steps
Potential Energy  =  0.000e+00
Maximum force =  0.000e+00 on atom 0
Norm of force =  0.000e+00

NOTE: 7 % of the run time was spent communicating energies,
  you might want to use the -nosum option of mdrun


gcq#320: "Do You Have Sex Maniacs or Schizophrenics or Astrophysicists  
in Your Family?" (Gogol Bordello)


The minimum is reached without steps, so... I don't know if the single  
atom minimization wors or not...


Valerio



"Justin A. Lemkul"  ha scritto:




vferra...@units.it wrote:

Dear all,
I'm dealing with a simulation of a polymer in CHCL3, the polymer  
works good, but I have some problems with the CHCL3 definition in  
GROMOS 53a6 ff.

I've taken the CHCL3 definition from the automated topology builder website:

http://compbio.biosci.uq.edu.au/atb/download.py?molid=1597&file=itp_uniatom

So the itp file of my CHCL3 definition is:

[ moleculetype ]
; Namenrexcl
CLF 3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass  
 typeBchargeB  massB
1CCL  1CLFCCl  1  0.179 12.011   
 ; qtot 0.179
2HCL  1CLFHCl  1  0.082  1.008   
 ; qtot 0.261
3   CLCL  1CLFCL1  1 -0.087 35.453   
 ; qtot 0.174
4   CLCL  1CLFCL2  1 -0.087 35.453   
 ; qtot 0.087
5   CLCL  1CLFCL3  1 -0.087 35.453   
 ; qtot 0


[ constraints ]
   1 3 1 0.1758
   1 4 1 0.1758
   1 5 1 0.1758
   2 3 1 0.233839
   2 4 1 0.233839
   2 5 1 0.233839
   3 4 1 0.290283
   3 5 1 0.290283
   4 5 1 0.290283

I've generated a box of solvent, but when I try to minimize it with  
the following mdp file:


title= Minimization
cpp= /lib/cpp
include= -I../top
constraints = none
integrator= steep
emtol= 2.5
emstep  = 0.01
nsteps= 10
nbfgscorr   = 10
nstenergy= 100
nstxtcout= 0
xtc_grps= system
energygrps= system
nstlist= 5


For EM, nstlist should be 1.


ns_type= grid
pbc = xyz
rlist= 1.0
coulombtype= cut-off


Plain cutoffs lead to bad artifacts and thus should generally not be used.


rcoulomb= 1.0
vdwtype = cut-off
rvdw= 1.4
fourierspacing= 0.15
fourier_nx  = 0
fourier_ny  = 0
fourier_nz  = 0
pme_order   = 4
optimize_fft= yes
tcoupl  = no
pcoupl  = no
gen_vel = no
constraint_algorithm= LINCS
lincs_order = 8
lincs_iter  = 2
nstlog  = 100
lincs_warnangle = 90

The system crash giving me the following error:

Fatal error:
Too many LINCS warnings (1413)
If you know what you are doing you can adjust the lincs warning  
threshold in your mdp file

or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem

My question is: why the system crash and why LINCS warnings are  
generated if all the molecule is constrained? What shell I do to  
avoid these probles? New CHCL3 definition?


The charges and atom types match exactly what the force field  
prescribes, so those are probably solid.


You need to simplify the problem.  You built a box, but it is  
failing.  Does an EM of a single molecule work, or does it fail as  
well?  Consult the following:


http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

-Justin

Re: [gmx-users] Re: change in secondary structure

[bharat gupta]

Sorry to ask this question but setting the gen_vel=yes and gen_seed = -1
will eventually lead to different simulation and thus different simulated
structures ?? .. and after completing one set of simulation with this
paramter and 3ns time .. do i have to repeat it some 3 or more times ??
pls comment.. as  I am going to start simulation with these parameters.

On Wed, Feb 2, 2011 at 5:27 AM, Justin A. Lemkul  wrote:

>
>
> bharat gupta wrote:
>
>> Thanks for such a detailed reply to my queries .. But conducting a 50ns
>> simulation will take time ... so i want to conduct independent simulation
>> and for that I searched some threads but was not able to get the proper
>> description and method... if u can guide me through an appropriate link ..
>> it would be much more helpful ..
>>
>
> Each simulation begins with the assignment of random velocities (gen_vel =
> yes).  Specify different values of gen_seed (or leave it set to -1) to get
> different velocities each time.
>
> -Justin
>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com
-- 
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Re: [gmx-users] links warnangles

[Justin A. Lemkul]

vferra...@units.it wrote:

I've just tried with a single CHCL3 molecule, here's the output:

Back Off! I just backed up md.log to ./#md.log.2#
Getting Loaded...
Reading file clfmin.tpr, VERSION 4.0.7 (single precision)
Loaded with Money

NNODES=2, MYRANK=1, HOSTNAME=biohazard
NODEID=1 argc=6
Making 1D domain decomposition 2 x 1 x 1

Step -1, time -0.001 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 301.323604, max 324.810791 (between atoms 1 and 3)
bonds that rotated more than 90 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Back Off! I just backed up step-1b_n1.pdb to ./#step-1b_n1.pdb.2#

Back Off! I just backed up step-1c_n1.pdb to ./#step-1c_n1.pdb.2#
Wrote pdb files with previous and current coordinates

Back Off! I just backed up traj.trr to ./#traj.trr.1#

Back Off! I just backed up ener.edr to ./#ener.edr.2#
Steepest Descents:
   Tolerance (Fmax)   =  2.5e+00
   Number of steps=   10
Step=0, Dmax= 1.0e-02 nm, Epot=  0.0e+00 Fmax= 0.0e+00, atom= 0

writing lowest energy coordinates.

Back Off! I just backed up clfmin.gro to ./#clfmin.gro.1#

Steepest Descents converged to Fmax < 2.5 in 1 steps
Potential Energy  =  0.000e+00
Maximum force =  0.000e+00 on atom 0
Norm of force =  0.000e+00

NOTE: 7 % of the run time was spent communicating energies,
  you might want to use the -nosum option of mdrun


gcq#320: "Do You Have Sex Maniacs or Schizophrenics or Astrophysicists 
in Your Family?" (Gogol Bordello)


The minimum is reached without steps, so... I don't know if the single 
atom minimization wors or not...




It certainly didn't work.  At the outset of the process, you instantly got a 
LINCS warning, indicating instability.  This would indicate to me that the model 
itself is unstable.  I'm sorry to say I don't know what to suggest, as the 
Gromos96 chloroform model should be rigid, and your topology reproduces what is 
in the force field .rtp entry for chloroform.


-Justin


Valerio



"Justin A. Lemkul"  ha scritto:




vferra...@units.it wrote:

Dear all,
I'm dealing with a simulation of a polymer in CHCL3, the polymer 
works good, but I have some problems with the CHCL3 definition in 
GROMOS 53a6 ff.
I've taken the CHCL3 definition from the automated topology builder 
website:


http://compbio.biosci.uq.edu.au/atb/download.py?molid=1597&file=itp_uniatom 



So the itp file of my CHCL3 definition is:

[ moleculetype ]
; Namenrexcl
CLF 3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass 
 typeBchargeB  massB
1CCL  1CLFCCl  1  0.179 12.011  
 ; qtot 0.179
2HCL  1CLFHCl  1  0.082  1.008  
 ; qtot 0.261
3   CLCL  1CLFCL1  1 -0.087 35.453  
 ; qtot 0.174
4   CLCL  1CLFCL2  1 -0.087 35.453  
 ; qtot 0.087
5   CLCL  1CLFCL3  1 -0.087 35.453  
 ; qtot 0


[ constraints ]
   1 3 1 0.1758
   1 4 1 0.1758
   1 5 1 0.1758
   2 3 1 0.233839
   2 4 1 0.233839
   2 5 1 0.233839
   3 4 1 0.290283
   3 5 1 0.290283
   4 5 1 0.290283

I've generated a box of solvent, but when I try to minimize it with 
the following mdp file:


title= Minimization
cpp= /lib/cpp
include= -I../top
constraints = none
integrator= steep
emtol= 2.5
emstep  = 0.01
nsteps= 10
nbfgscorr   = 10
nstenergy= 100
nstxtcout= 0
xtc_grps= system
energygrps= system
nstlist= 5


For EM, nstlist should be 1.


ns_type= grid
pbc = xyz
rlist= 1.0
coulombtype= cut-off


Plain cutoffs lead to bad artifacts and thus should generally not be 
used.



rcoulomb= 1.0
vdwtype = cut-off
rvdw= 1.4
fourierspacing= 0.15
fourier_nx  = 0
fourier_ny  = 0
fourier_nz  = 0
pme_order   = 4
optimize_fft= yes
tcoupl  = no
pcoupl  = no
gen_vel = no
constraint_algorithm= LINCS
lincs_order = 8
lincs_iter  = 2
nstlog  = 100
lincs_warnangle = 90

The system crash giving me the following error:

Fatal error:
Too many LINCS warnings (1413)
If you know what you are doing you can adjust the lincs warning 
threshold in your mdp file

or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem

My question is: why the system crash and why LINCS warnings are 
generated if all the molecule is constrained? What shell I do to 
avoid these probl

Re: [gmx-users] Re: change in secondary structure

[Justin A. Lemkul]

bharat gupta wrote:
Sorry to ask this question but setting the gen_vel=yes and gen_seed = -1 
will eventually lead to different simulation and thus different 
simulated structures ?? .. and after completing one set of simulation 
with this paramter and 3ns time .. do i have to repeat it some 3 or more 
times ?? pls comment.. as  I am going to start simulation with these 
parameters.




As I have already said, the combination of velocity generation with a different 
random seed will give you (in theory) independent trajectories.  How many 
replicates you run is up to you.  I certainly hope that, after all I've said, 
you're still not intending on simply running 3-ns simulations, regardless of how 
many replicates you run.  If you're looking at loop movements, you won't answer 
your questions with such little data.


-Justin

On Wed, Feb 2, 2011 at 5:27 AM, Justin A. Lemkul > wrote:




bharat gupta wrote:

Thanks for such a detailed reply to my queries .. But conducting
a 50ns simulation will take time ... so i want to conduct
independent simulation and for that I searched some threads but
was not able to get the proper description and method... if u
can guide me through an appropriate link .. it would be much
more helpful ..


Each simulation begins with the assignment of random velocities
(gen_vel = yes).  Specify different values of gen_seed (or leave it
set to -1) to get different velocities each time.

-Justin


-- 



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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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www
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.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists




--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.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 listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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Re: [gmx-users] links warnangles

[Justin A. Lemkul]

Justin A. Lemkul wrote:



vferra...@units.it wrote:

I've just tried with a single CHCL3 molecule, here's the output:

Back Off! I just backed up md.log to ./#md.log.2#
Getting Loaded...
Reading file clfmin.tpr, VERSION 4.0.7 (single precision)
Loaded with Money

NNODES=2, MYRANK=1, HOSTNAME=biohazard
NODEID=1 argc=6
Making 1D domain decomposition 2 x 1 x 1

Step -1, time -0.001 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 301.323604, max 324.810791 (between atoms 1 and 3)
bonds that rotated more than 90 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Back Off! I just backed up step-1b_n1.pdb to ./#step-1b_n1.pdb.2#

Back Off! I just backed up step-1c_n1.pdb to ./#step-1c_n1.pdb.2#
Wrote pdb files with previous and current coordinates

Back Off! I just backed up traj.trr to ./#traj.trr.1#

Back Off! I just backed up ener.edr to ./#ener.edr.2#
Steepest Descents:
   Tolerance (Fmax)   =  2.5e+00
   Number of steps=   10
Step=0, Dmax= 1.0e-02 nm, Epot=  0.0e+00 Fmax= 0.0e+00, 
atom= 0


writing lowest energy coordinates.

Back Off! I just backed up clfmin.gro to ./#clfmin.gro.1#

Steepest Descents converged to Fmax < 2.5 in 1 steps
Potential Energy  =  0.000e+00
Maximum force =  0.000e+00 on atom 0
Norm of force =  0.000e+00

NOTE: 7 % of the run time was spent communicating energies,
  you might want to use the -nosum option of mdrun


gcq#320: "Do You Have Sex Maniacs or Schizophrenics or Astrophysicists 
in Your Family?" (Gogol Bordello)


The minimum is reached without steps, so... I don't know if the single 
atom minimization wors or not...




It certainly didn't work.  At the outset of the process, you instantly 
got a LINCS warning, indicating instability.  This would indicate to me 
that the model itself is unstable.  I'm sorry to say I don't know what 
to suggest, as the Gromos96 chloroform model should be rigid, and your 
topology reproduces what is in the force field .rtp entry for chloroform.




I guess I'm blaming this all on the topology, but it could also be that your 
coordinates are messed up and they can't be resolved by EM.  Check into that, as 
well.


-Justin

--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

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

Re: [gmx-users] Re: change in secondary structure

[bharat gupta]

Sorry to make this point here but running a 50ns simulation will take
roughly 1 month on my system but a 10ns simulation will take 5 days on my
system .. so would a 10ns be enough to monitor such motions .. also i
request to u guide me to a link where I can find more about this independent
simulation and how to run many replicates & analyze them ?? .

On Wed, Feb 2, 2011 at 5:42 AM, Justin A. Lemkul  wrote:

>
>
> bharat gupta wrote:
>
>> Sorry to ask this question but setting the gen_vel=yes and gen_seed = -1
>> will eventually lead to different simulation and thus different simulated
>> structures ?? .. and after completing one set of simulation with this
>> paramter and 3ns time .. do i have to repeat it some 3 or more times ??
>> pls comment.. as  I am going to start simulation with these parameters.
>>
>>
> As I have already said, the combination of velocity generation with a
> different random seed will give you (in theory) independent trajectories.
>  How many replicates you run is up to you.  I certainly hope that, after all
> I've said, you're still not intending on simply running 3-ns simulations,
> regardless of how many replicates you run.  If you're looking at loop
> movements, you won't answer your questions with such little data.
>
> -Justin
>
>  On Wed, Feb 2, 2011 at 5:27 AM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>bharat gupta wrote:
>>
>>Thanks for such a detailed reply to my queries .. But conducting
>>a 50ns simulation will take time ... so i want to conduct
>>independent simulation and for that I searched some threads but
>>was not able to get the proper description and method... if u
>>can guide me through an appropriate link .. it would be much
>>more helpful ..
>>
>>
>>Each simulation begins with the assignment of random velocities
>>(gen_vel = yes).  Specify different values of gen_seed (or leave it
>>set to -1) to get different velocities each time.
>>
>>-Justin
>>
>>
>>-- 
>>
>>Justin A. Lemkul
>>Ph.D. Candidate
>>ICTAS Doctoral Scholar
>>MILES-IGERT Trainee
>>Department of Biochemistry
>>Virginia Tech
>>Blacksburg, VA
>>jalemkul[at]vt.edu  | (540) 231-9080
>>
>>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>
>>-- gmx-users mailing listgmx-users@gromacs.org
>>
>>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at
>>http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>Please don't post (un)subscribe requests to the list. Use the www
>>interface or send it to gmx-users-requ...@gromacs.org
>>.
>>
>>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
>>
>> --
>> Bharat
>> Ph.D. Candidate
>> Room No. : 7202A, 2nd Floor
>> Biomolecular Engineering Laboratory
>> Division of Chemical Engineering and Polymer Science
>> Pusan National University
>> Busan -609735
>> South Korea
>> Lab phone no. - +82-51-510-3680, +82-51-583-8343
>> Mobile no. - 010-5818-3680
>> E-mail : monu46...@yahoo.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 listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com
-- 
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Re: [gmx-users] Re: change in secondary structure

[Justin A. Lemkul]

bharat gupta wrote:
Sorry to make this point here but running a 50ns simulation will take 
roughly 1 month on my system but a 10ns simulation will take 5 days on 


A month is a reasonable time investment for quality MD simulations.

my system .. so would a 10ns be enough to monitor such motions .. also i 


Very doubtful, but I'm not going to speculate further.  You have to be willing 
to put in significant effort to answer complex questions, unless you're happy to 
settle for potentially unreliable data.


request to u guide me to a link where I can find more about this 
independent simulation and how to run many replicates & analyze them ??


There's nothing left to say.  I've told you how to initiate independent 
simulations.  Analyzing them is up to you based on your plans for this project. 
 No one on this list is going to provide you broad-reaching how-to's for doing 
anything you might come up with.  The manual is extensive, and the website/wiki 
has lots of tips and information.


-Justin

. 

On Wed, Feb 2, 2011 at 5:42 AM, Justin A. Lemkul > wrote:




bharat gupta wrote:

Sorry to ask this question but setting the gen_vel=yes and
gen_seed = -1 will eventually lead to different simulation and
thus different simulated structures ?? .. and after completing
one set of simulation with this paramter and 3ns time .. do i
have to repeat it some 3 or more times ?? pls comment.. as
 I am going to start simulation with these parameters.


As I have already said, the combination of velocity generation with
a different random seed will give you (in theory) independent
trajectories.  How many replicates you run is up to you.  I
certainly hope that, after all I've said, you're still not intending
on simply running 3-ns simulations, regardless of how many
replicates you run.  If you're looking at loop movements, you won't
answer your questions with such little data.

-Justin

On Wed, Feb 2, 2011 at 5:27 AM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   bharat gupta wrote:

   Thanks for such a detailed reply to my queries .. But
conducting
   a 50ns simulation will take time ... so i want to conduct
   independent simulation and for that I searched some
threads but
   was not able to get the proper description and method... if u
   can guide me through an appropriate link .. it would be much
   more helpful ..


   Each simulation begins with the assignment of random velocities
   (gen_vel = yes).  Specify different values of gen_seed (or
leave it
   set to -1) to get different velocities each time.

   -Justin


   -- 

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

   http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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

   >

   http://lists.gromacs.org/mailman/listinfo/gmx-users
   Please search the archive at
   http://www.gromacs.org/Support/Mailing_Lists/Search before
posting!
   Please don't post (un)subscribe requests to the list. Use the www
   interface or send it to gmx-users-requ...@gromacs.org

   >.

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




-- 
Bharat

Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.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

Re: [gmx-users] Re: change in secondary structure

[bharat gupta]

Anyways thanks for ur detailed answers .. After completing the simulation ,
the 10ns one I will get back to u if any doubt arises .. Also I am running a
3ns simulation of the same variant of GFP but with a different FF ... hoping
to get any positive result for that one ...

On Wed, Feb 2, 2011 at 5:54 AM, Justin A. Lemkul  wrote:

>
>
> bharat gupta wrote:
>
>> Sorry to make this point here but running a 50ns simulation will take
>> roughly 1 month on my system but a 10ns simulation will take 5 days on
>>
>
> A month is a reasonable time investment for quality MD simulations.
>
>
>  my system .. so would a 10ns be enough to monitor such motions .. also i
>>
>
> Very doubtful, but I'm not going to speculate further.  You have to be
> willing to put in significant effort to answer complex questions, unless
> you're happy to settle for potentially unreliable data.
>
>
>  request to u guide me to a link where I can find more about this
>> independent simulation and how to run many replicates & analyze them ??
>>
>
> There's nothing left to say.  I've told you how to initiate independent
> simulations.  Analyzing them is up to you based on your plans for this
> project.  No one on this list is going to provide you broad-reaching
> how-to's for doing anything you might come up with.  The manual is
> extensive, and the website/wiki has lots of tips and information.
>
> -Justin
>
>  .
>> On Wed, Feb 2, 2011 at 5:42 AM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>bharat gupta wrote:
>>
>>Sorry to ask this question but setting the gen_vel=yes and
>>gen_seed = -1 will eventually lead to different simulation and
>>thus different simulated structures ?? .. and after completing
>>one set of simulation with this paramter and 3ns time .. do i
>>have to repeat it some 3 or more times ?? pls comment.. as
>> I am going to start simulation with these parameters.
>>
>>
>>As I have already said, the combination of velocity generation with
>>a different random seed will give you (in theory) independent
>>trajectories.  How many replicates you run is up to you.  I
>>certainly hope that, after all I've said, you're still not intending
>>on simply running 3-ns simulations, regardless of how many
>>replicates you run.  If you're looking at loop movements, you won't
>>answer your questions with such little data.
>>
>>-Justin
>>
>>On Wed, Feb 2, 2011 at 5:27 AM, Justin A. Lemkul
>>mailto:jalem...@vt.edu>
>>>> wrote:
>>
>>
>>
>>   bharat gupta wrote:
>>
>>   Thanks for such a detailed reply to my queries .. But
>>conducting
>>   a 50ns simulation will take time ... so i want to conduct
>>   independent simulation and for that I searched some
>>threads but
>>   was not able to get the proper description and method... if
>> u
>>   can guide me through an appropriate link .. it would be much
>>   more helpful ..
>>
>>
>>   Each simulation begins with the assignment of random velocities
>>   (gen_vel = yes).  Specify different values of gen_seed (or
>>leave it
>>   set to -1) to get different velocities each time.
>>
>>   -Justin
>>
>>
>>   -- 
>>
>>   Justin A. Lemkul
>>   Ph.D. Candidate
>>   ICTAS Doctoral Scholar
>>   MILES-IGERT Trainee
>>   Department of Biochemistry
>>   Virginia Tech
>>   Blacksburg, VA
>>   jalemkul[at]vt.edu   | (540)
>>
>>231-9080
>>
>>   http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>   
>>   -- gmx-users mailing listgmx-users@gromacs.org
>>
>>   >
>>
>>
>>   http://lists.gromacs.org/mailman/listinfo/gmx-users
>>   Please search the archive at
>>   http://www.gromacs.org/Support/Mailing_Lists/Search before
>>posting!
>>   Please don't post (un)subscribe requests to the list. Use the
>> www
>>   interface or send it to gmx-users-requ...@gromacs.org
>>
>>   >>.
>>
>>   Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
>>
>>-- Bharat
>>Ph.D. Candidate
>>Room No. : 7202A, 2nd Floor
>>Biomolecular Engineering Laboratory
>>Division of Chemical Engineering and Polymer Science
>>Pusan National University
>>Busan -609735
>>South Korea
>>Lab phone no. - +82-51-510-3680, +82-51-583-8343

Re: [gmx-users] links warnangles

[vferrario]

The molecule is rigid because it's all constrained and the coordinates  
of the single molecule seem to be ok:


CLF
5
1CLFCCl1   3.041   1.571   0.924
1CLFHCl2   3.001   1.637   0.845
1CLFCL13   3.071   1.661   1.073
1CLFCL24   3.186   1.493   0.867
1CLFCL35   2.916   1.452   0.963
   0.5   0.5   0.5

I've found another CHCL3 model on the GROMACS website by user  
contribution, but the difinition is closed to mine, exept for the  
hydrogen atom which is not considered as an independent particle but  
is considered with the carbon:


[ atomtypes ]

;typemasscharge   ptype  sigma  epsilon

 CH  12.01100   0.420   A3.8e-01  3.26944e-01

 CLCL3   35.45300  -0.140   A3.47000e-01  1.25604e+00



[ moleculetype ]

; name  nrexcl

CCl3  3



[ atoms ]

;   nr   type   resnr  residu  atomcgnrcharge

1  CH1  CCl4CT1 10.420

2  CLCL3 1  CCl4Cl2 1   -0.140

3  CLCL3 1  CCl4Cl3 1   -0.140

4  CLCL3 1  CCl4Cl4 1   -0.140





[ constraints ]

;  aiaj functb0

1 2 1 0.17580

1 3 1 0.17580

1 4 1 0.17580

2 3 1 0.2902831

2 4 1 0.2902831

3 4 1 0.2902831


Probably is the definition of that single hydrogen that cause  
problems, I'll check this new definition.


Valerio


"Justin A. Lemkul"  ha scritto:




Justin A. Lemkul wrote:



vferra...@units.it wrote:

I've just tried with a single CHCL3 molecule, here's the output:

Back Off! I just backed up md.log to ./#md.log.2#
Getting Loaded...
Reading file clfmin.tpr, VERSION 4.0.7 (single precision)
Loaded with Money

NNODES=2, MYRANK=1, HOSTNAME=biohazard
NODEID=1 argc=6
Making 1D domain decomposition 2 x 1 x 1

Step -1, time -0.001 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 301.323604, max 324.810791 (between atoms 1 and 3)
bonds that rotated more than 90 degrees:
atom 1 atom 2  angle  previous, current, constraint length

Back Off! I just backed up step-1b_n1.pdb to ./#step-1b_n1.pdb.2#

Back Off! I just backed up step-1c_n1.pdb to ./#step-1c_n1.pdb.2#
Wrote pdb files with previous and current coordinates

Back Off! I just backed up traj.trr to ./#traj.trr.1#

Back Off! I just backed up ener.edr to ./#ener.edr.2#
Steepest Descents:
  Tolerance (Fmax)   =  2.5e+00
  Number of steps=   10
Step=0, Dmax= 1.0e-02 nm, Epot=  0.0e+00 Fmax= 0.0e+00, atom= 0

writing lowest energy coordinates.

Back Off! I just backed up clfmin.gro to ./#clfmin.gro.1#

Steepest Descents converged to Fmax < 2.5 in 1 steps
Potential Energy  =  0.000e+00
Maximum force =  0.000e+00 on atom 0
Norm of force =  0.000e+00

NOTE: 7 % of the run time was spent communicating energies,
 you might want to use the -nosum option of mdrun


gcq#320: "Do You Have Sex Maniacs or Schizophrenics or  
Astrophysicists in Your Family?" (Gogol Bordello)


The minimum is reached without steps, so... I don't know if the  
single atom minimization wors or not...




It certainly didn't work.  At the outset of the process, you  
instantly got a LINCS warning, indicating instability.  This would  
indicate to me that the model itself is unstable.  I'm sorry to say  
I don't know what to suggest, as the Gromos96 chloroform model  
should be rigid, and your topology reproduces what is in the force  
field .rtp entry for chloroform.




I guess I'm blaming this all on the topology, but it could also be  
that your coordinates are messed up and they can't be resolved by  
EM.  Check into that, as well.


-Justin

--


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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Please search the archive at  
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Re: [gmx-users] links warnangles

[vferrario]

Seems that the new definition I've found works, but it is still  
unclear to me why...


Valerio


vferra...@units.it ha scritto:

The molecule is rigid because it's all constrained and the  
coordinates of the single molecule seem to be ok:


CLF
5
1CLFCCl1   3.041   1.571   0.924
1CLFHCl2   3.001   1.637   0.845
1CLFCL13   3.071   1.661   1.073
1CLFCL24   3.186   1.493   0.867
1CLFCL35   2.916   1.452   0.963
   0.5   0.5   0.5

I've found another CHCL3 model on the GROMACS website by user  
contribution, but the difinition is closed to mine, exept for the  
hydrogen atom which is not considered as an independent particle but  
is considered with the carbon:


[ atomtypes ]

;typemasscharge   ptype  sigma  epsilon

 CH  12.01100   0.420   A3.8e-01  3.26944e-01

 CLCL3   35.45300  -0.140   A3.47000e-01  1.25604e+00



[ moleculetype ]

; name  nrexcl

CCl3  3



[ atoms ]

;   nr   type   resnr  residu  atomcgnrcharge

1  CH1  CCl4CT1 10.420

2  CLCL3 1  CCl4Cl2 1   -0.140

3  CLCL3 1  CCl4Cl3 1   -0.140

4  CLCL3 1  CCl4Cl4 1   -0.140





[ constraints ]

;  aiaj functb0

1 2 1 0.17580

1 3 1 0.17580

1 4 1 0.17580

2 3 1 0.2902831

2 4 1 0.2902831

3 4 1 0.2902831


Probably is the definition of that single hydrogen that cause  
problems, I'll check this new definition.


Valerio


"Justin A. Lemkul"  ha scritto:




Justin A. Lemkul wrote:



vferra...@units.it wrote:

I've just tried with a single CHCL3 molecule, here's the output:

Back Off! I just backed up md.log to ./#md.log.2#
Getting Loaded...
Reading file clfmin.tpr, VERSION 4.0.7 (single precision)
Loaded with Money

NNODES=2, MYRANK=1, HOSTNAME=biohazard
NODEID=1 argc=6
Making 1D domain decomposition 2 x 1 x 1

Step -1, time -0.001 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 301.323604, max 324.810791 (between atoms 1 and 3)
bonds that rotated more than 90 degrees:
atom 1 atom 2  angle  previous, current, constraint length

Back Off! I just backed up step-1b_n1.pdb to ./#step-1b_n1.pdb.2#

Back Off! I just backed up step-1c_n1.pdb to ./#step-1c_n1.pdb.2#
Wrote pdb files with previous and current coordinates

Back Off! I just backed up traj.trr to ./#traj.trr.1#

Back Off! I just backed up ener.edr to ./#ener.edr.2#
Steepest Descents:
 Tolerance (Fmax)   =  2.5e+00
 Number of steps=   10
Step=0, Dmax= 1.0e-02 nm, Epot=  0.0e+00 Fmax=  
0.0e+00, atom= 0


writing lowest energy coordinates.

Back Off! I just backed up clfmin.gro to ./#clfmin.gro.1#

Steepest Descents converged to Fmax < 2.5 in 1 steps
Potential Energy  =  0.000e+00
Maximum force =  0.000e+00 on atom 0
Norm of force =  0.000e+00

NOTE: 7 % of the run time was spent communicating energies,
you might want to use the -nosum option of mdrun


gcq#320: "Do You Have Sex Maniacs or Schizophrenics or  
Astrophysicists in Your Family?" (Gogol Bordello)


The minimum is reached without steps, so... I don't know if the  
single atom minimization wors or not...




It certainly didn't work.  At the outset of the process, you  
instantly got a LINCS warning, indicating instability.  This would  
indicate to me that the model itself is unstable.  I'm sorry to  
say I don't know what to suggest, as the Gromos96 chloroform model  
should be rigid, and your topology reproduces what is in the force  
field .rtp entry for chloroform.




I guess I'm blaming this all on the topology, but it could also be  
that your coordinates are messed up and they can't be resolved by  
EM.  Check into that, as well.


-Justin

--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at  
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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Re: [gmx-users] links warnangles

[Justin A. Lemkul]

vferra...@units.it wrote:
Seems that the new definition I've found works, but it is still unclear 
to me why...




There was a post long ago that I seem to remember reported the same problem. 
Since there is no true bond between H and C, the H position is basically 
triangulated by all of the other atoms.  There should not be a bond between H 
and C, since it should be constrained, yielding too many degrees of freedom. 
Seems to me that these rigid Gromos96 solvent models are a little strange.


-Justin


Valerio


vferra...@units.it ha scritto:

The molecule is rigid because it's all constrained and the coordinates 
of the single molecule seem to be ok:


CLF
5
1CLFCCl1   3.041   1.571   0.924
1CLFHCl2   3.001   1.637   0.845
1CLFCL13   3.071   1.661   1.073
1CLFCL24   3.186   1.493   0.867
1CLFCL35   2.916   1.452   0.963
   0.5   0.5   0.5

I've found another CHCL3 model on the GROMACS website by user 
contribution, but the difinition is closed to mine, exept for the 
hydrogen atom which is not considered as an independent particle but 
is considered with the carbon:


[ atomtypes ]

;typemasscharge   ptype  sigma  epsilon

 CH  12.01100   0.420   A3.8e-01  3.26944e-01

 CLCL3   35.45300  -0.140   A3.47000e-01  1.25604e+00



[ moleculetype ]

; name  nrexcl

CCl3  3



[ atoms ]

;   nr   type   resnr  residu  atomcgnrcharge

1  CH1  CCl4CT1 10.420

2  CLCL3 1CCl4Cl21-0.140

3  CLCL3 1CCl4Cl31-0.140

4  CLCL3 1CCl4Cl41-0.140





[ constraints ]

;  aiaj functb0

1 2 1 0.17580

1 3 1 0.17580

1 4 1 0.17580

2 3 1 0.2902831

2 4 1 0.2902831

3 4 1 0.2902831


Probably is the definition of that single hydrogen that cause 
problems, I'll check this new definition.


Valerio


"Justin A. Lemkul"  ha scritto:




Justin A. Lemkul wrote:



vferra...@units.it wrote:

I've just tried with a single CHCL3 molecule, here's the output:

Back Off! I just backed up md.log to ./#md.log.2#
Getting Loaded...
Reading file clfmin.tpr, VERSION 4.0.7 (single precision)
Loaded with Money

NNODES=2, MYRANK=1, HOSTNAME=biohazard
NODEID=1 argc=6
Making 1D domain decomposition 2 x 1 x 1

Step -1, time -0.001 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 301.323604, max 324.810791 (between atoms 1 and 3)
bonds that rotated more than 90 degrees:
atom 1 atom 2  angle  previous, current, constraint length

Back Off! I just backed up step-1b_n1.pdb to ./#step-1b_n1.pdb.2#

Back Off! I just backed up step-1c_n1.pdb to ./#step-1c_n1.pdb.2#
Wrote pdb files with previous and current coordinates

Back Off! I just backed up traj.trr to ./#traj.trr.1#

Back Off! I just backed up ener.edr to ./#ener.edr.2#
Steepest Descents:
 Tolerance (Fmax)   =  2.5e+00
 Number of steps=   10
Step=0, Dmax= 1.0e-02 nm, Epot=  0.0e+00 Fmax= 0.0e+00, 
atom= 0


writing lowest energy coordinates.

Back Off! I just backed up clfmin.gro to ./#clfmin.gro.1#

Steepest Descents converged to Fmax < 2.5 in 1 steps
Potential Energy  =  0.000e+00
Maximum force =  0.000e+00 on atom 0
Norm of force =  0.000e+00

NOTE: 7 % of the run time was spent communicating energies,
you might want to use the -nosum option of mdrun


gcq#320: "Do You Have Sex Maniacs or Schizophrenics or 
Astrophysicists in Your Family?" (Gogol Bordello)


The minimum is reached without steps, so... I don't know if the 
single atom minimization wors or not...




It certainly didn't work.  At the outset of the process, you 
instantly got a LINCS warning, indicating instability.  This would 
indicate to me that the model itself is unstable.  I'm sorry to say 
I don't know what to suggest, as the Gromos96 chloroform model 
should be rigid, and your topology reproduces what is in the force 
field .rtp entry for chloroform.




I guess I'm blaming this all on the topology, but it could also be 
that your coordinates are messed up and they can't be resolved by 
EM.  Check into that, as well.


-Justin

--


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] links warnangles

[vferrario]

No, is not working also in this case... probably the problem is with  
my mdp files:


for minimization is:

title   = Minimization
cpp = /lib/cpp
include = -I../top
constraints = none
integrator  = steep
emtol   = 5.0
emstep  = 0.01
nsteps  = 10
nbfgscorr   = 10
nstenergy   = 100
nstxtcout   = 0
xtc_grps= system
energygrps  = system
nstlist = 5
ns_type = grid
pbc = xyz
rlist   = 1.0
coulombtype = PME
rcoulomb= 1.0
vdwtype = cut-off
rvdw= 1.4
fourierspacing  = 0.15
fourier_nx  = 0
fourier_ny  = 0
fourier_nz  = 0
pme_order   = 4
optimize_fft= yes
tcoupl  = no
pcoupl  = no
gen_vel = no
constraint_algorithm= LINCS
lincs_order = 8
lincs_iter  = 2
nstlog  = 100
lincs_warnangle = 90

and for dynamic:

title= dinamica
;Preprocessor
cpp  = /lib/cpp
;Directories to include in the topology format
include  = -I../top
;Run control: A leap-frog algorithm for integrating Newton's equations.
integrator   = md
:time step in femtoseconds
dt   = 0.002
;number of steps
nsteps   = 50
;frequency to write coordinates to output trajectory file
nstxout  = 100
;frequency to write velocities to output trajectory file
nstvout  = 100
;frequency to write energies to log file
nstlog   = 100
;frequency to write energies to energy file
nstenergy= 100
;frequency to write coordinates to xtc trajectory
nstxtcout= 100
;group(s) to write to xtc trajectory
xtc_grps = system
;group(s) to write to energy file
energygrps   = system
;Frequency to update the neighbor list (and the long-range forces,
;when using twin-range cut-off's).
nstlist  = 100
;Make a grid in the box and only check atoms in neighboring grid cells
;when constructing a new neighbor list every nstlist steps.
ns_type  = grid
;cut-off distance for the short-range neighbor list
rlist= 1.4
;treatment of electrostatic interactions
coulombtype  = cut-off
rcoulomb = 1.4
;treatment of van der waals interactions
rvdw = 1.4
; Periodic boudary conditions in all the directions
pbc  = xyz
;Temperature coupling
tcoupl   = berendsen
tc-grps  = system
tau_t= 0.1
ref_t= 300
;Pressure coupling
Pcoupl   = berendsen
Pcoupltype   = isotropic
tau_p= 1.0
compressibility  = 3e-5
ref_p= 100
;Velocity generation
gen_vel  = yes
gen_temp = 300
gen_seed = 176458

Any ideas? Thanks a lot.

Valerio


vferra...@units.it ha scritto:

The molecule is rigid because it's all constrained and the  
coordinates of the single molecule seem to be ok:


CLF
5
1CLFCCl1   3.041   1.571   0.924
1CLFHCl2   3.001   1.637   0.845
1CLFCL13   3.071   1.661   1.073
1CLFCL24   3.186   1.493   0.867
1CLFCL35   2.916   1.452   0.963
   0.5   0.5   0.5

I've found another CHCL3 model on the GROMACS website by user  
contribution, but the difinition is closed to mine, exept for the  
hydrogen atom which is not considered as an independent particle but  
is considered with the carbon:


[ atomtypes ]

;typemasscharge   ptype  sigma  epsilon

 CH  12.01100   0.420   A3.8e-01  3.26944e-01

 CLCL3   35.45300  -0.140   A3.47000e-01  1.25604e+00



[ moleculetype ]

; name  nrexcl

CCl3  3



[ atoms ]

;   nr   type   resnr  residu  atomcgnrcharge

1  CH1  CCl4CT1 10.420

2  CLCL3 1  CCl4Cl2 1   -0.140

3  CLCL3 1  CCl4Cl3 1   -0.140

4  CLCL3 1  CCl4Cl4 1   -0.140





[ constraints ]

;  aiaj functb0

1 2 1 0.17580

1 3 1 0.17580

1 4 1 0.17580

2 3 1 0.2902831

2 4 1 0.2902831

3 4 1 0.2902831


Probably is the definition of that single hydrogen that cause  
problems, I'll check this new definition.


Valerio


"Justin A. Lemkul"  ha scritto:




Justin A. Lemkul wrote:



vferra...@units.it wrote:

I've just tried with a single CHCL3 molecule, here's the output:

Back Off! I just backed up md.log to ./#md.log.2#
Getting Loaded...
Reading file clfmin.tpr, VERSION 4.0.7 (single precision)
Loaded with Money

NNODES=2, MYRANK=1, HOSTNAME=biohazard
NODEID=1 argc=6
Making 1D domain decomposition 2 x 1 x 1

Step -1, time -0.

Re: [gmx-users] links warnangles

[Justin A. Lemkul]

vferra...@units.it wrote:
No, is not working also in this case... probably the problem is with my 
mdp files:




I would argue that it's the coordinates that are the problem.  For instance, 
compare the distances expected by the topology:


1 3 1 0.1758
1 4 1 0.1758
1 5 1 0.1758
2 3 1 0.233839
2 4 1 0.233839
2 5 1 0.233839
3 4 1 0.290283
3 5 1 0.290283
4 5 1 0.290283

with the actual distances found in the coordinate file:

1 3 1 0.177
1 4 1 0.177
1 5 1 0.174
2 3 1 0.240
2 4 1 0.235
2 5 1 0.235
3 4 1 0.282
3 5 1 0.290
4 5 1 0.289

The model requires 9 constraints to be satisfied in harmony.  If the starting 
geometry isn't perfect (or very close to it), there's probably too much 
rearranging required to make the model work.  Removal of the explicit H probably 
yielded a set of constraints that could be somewhat satisfied by EM, but fall 
apart in MD, which could be for a variety of reasons.


-Justin


for minimization is:

title= Minimization
cpp= /lib/cpp
include= -I../top
constraints = none
integrator= steep
emtol= 5.0
emstep  = 0.01
nsteps= 10
nbfgscorr   = 10
nstenergy= 100
nstxtcout= 0
xtc_grps= system
energygrps= system
nstlist= 5
ns_type= grid
pbc = xyz
rlist= 1.0
coulombtype= PME
rcoulomb= 1.0
vdwtype = cut-off
rvdw= 1.4
fourierspacing= 0.15
fourier_nx  = 0
fourier_ny  = 0
fourier_nz  = 0
pme_order   = 4
optimize_fft= yes
tcoupl  = no
pcoupl  = no
gen_vel = no
constraint_algorithm= LINCS
lincs_order = 8
lincs_iter  = 2
nstlog  = 100
lincs_warnangle = 90

and for dynamic:

title= dinamica
;Preprocessor
cpp = /lib/cpp
;Directories to include in the topology format
include  = -I../top
;Run control: A leap-frog algorithm for integrating Newton's equations.
integrator = md
:time step in femtoseconds
dt = 0.002
;number of steps
nsteps   = 50
;frequency to write coordinates to output trajectory file
nstxout  = 100
;frequency to write velocities to output trajectory file
nstvout  = 100
;frequency to write energies to log file
nstlog   = 100
;frequency to write energies to energy file
nstenergy = 100
;frequency to write coordinates to xtc trajectory
nstxtcout = 100
;group(s) to write to xtc trajectory
xtc_grps = system
;group(s) to write to energy file
energygrps = system
;Frequency to update the neighbor list (and the long-range forces,
;when using twin-range cut-off's).
nstlist  = 100
;Make a grid in the box and only check atoms in neighboring grid cells
;when constructing a new neighbor list every nstlist steps.
ns_type  = grid
;cut-off distance for the short-range neighbor list
rlist = 1.4
;treatment of electrostatic interactions
coulombtype = cut-off
rcoulomb = 1.4
;treatment of van der waals interactions
rvdw = 1.4
; Periodic boudary conditions in all the directions
pbc  = xyz
;Temperature coupling
tcoupl   = berendsen
tc-grps  = system
tau_t = 0.1
ref_t = 300
;Pressure coupling
Pcoupl   = berendsen
Pcoupltype   = isotropic
tau_p = 1.0
compressibility  = 3e-5
ref_p = 100
;Velocity generation
gen_vel  = yes
gen_temp = 300
gen_seed = 176458

Any ideas? Thanks a lot.

Valerio


vferra...@units.it ha scritto:

The molecule is rigid because it's all constrained and the coordinates 
of the single molecule seem to be ok:


CLF
5
1CLFCCl1   3.041   1.571   0.924
1CLFHCl2   3.001   1.637   0.845
1CLFCL13   3.071   1.661   1.073
1CLFCL24   3.186   1.493   0.867
1CLFCL35   2.916   1.452   0.963
   0.5   0.5   0.5

I've found another CHCL3 model on the GROMACS website by user 
contribution, but the difinition is closed to mine, exept for the 
hydrogen atom which is not considered as an independent particle but 
is considered with the carbon:


[ atomtypes ]

;typemasscharge   ptype  sigma  epsilon

 CH  12.01100   0.420   A3.8e-01  3.26944e-01

 CLCL3   35.45300  -0.140   A3.47000e-01  1.25604e+00



[ moleculetype ]

; name  nrexcl

CCl3  3



[ atoms ]

;   nr   type   resnr  residu  atomcgnrcharge

1  CH1  CCl4CT1 10.420

2  CLCL3 1CCl4Cl21-0.140

3  CLCL3 1CCl4Cl3 

Re: [gmx-users] links warnangles

[Justin A. Lemkul]

Justin A. Lemkul wrote:



vferra...@units.it wrote:
No, is not working also in this case... probably the problem is with 
my mdp files:




I would argue that it's the coordinates that are the problem.  For 
instance, compare the distances expected by the topology:


1 3 1 0.1758
1 4 1 0.1758
1 5 1 0.1758
2 3 1 0.233839
2 4 1 0.233839
2 5 1 0.233839
3 4 1 0.290283
3 5 1 0.290283
4 5 1 0.290283

with the actual distances found in the coordinate file:

1 3 1 0.177
1 4 1 0.177
1 5 1 0.174
2 3 1 0.240
2 4 1 0.235
2 5 1 0.235
3 4 1 0.282
3 5 1 0.290
4 5 1 0.289

The model requires 9 constraints to be satisfied in harmony.  If the 
starting geometry isn't perfect (or very close to it), there's probably 
too much rearranging required to make the model work.  Removal of the 
explicit H probably yielded a set of constraints that could be somewhat 
satisfied by EM, but fall apart in MD, which could be for a variety of 
reasons.




I've obtained a stable trajectory for a single CHCL3 molecule.  By setting 
"continuation = no" (so that constraints are not solved before step 0) in the 
em.mdp file, and then reducing nstlist to 5 in md.mdp, I was able to run 100 ps 
of MD with no issue.  The value of nstlist is probably the cause of the crash 
you mention.  Updating the neighborlist every 200 fs is 10-20 times too long.


-Justin

--


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] links warnangles

[Justin A. Lemkul]

Justin A. Lemkul wrote:



I've obtained a stable trajectory for a single CHCL3 molecule.  By 
setting "continuation = no" (so that constraints are not solved before 
step 0) in the em.mdp file, and then reducing nstlist to 5 in md.mdp, I 


Ack, this should be "continuation = yes."  Sorry for the confusion.  I will copy 
from my .mdp file...I will copy from my .mdp file... :)


-Justin

--


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] error during installation of gromacs 4.5.3 on windows (cygwin platform)

[bharat gupta]

Hi,

I have installed gromacs 4.5.3 on windows and the installation was
successful but while running the pdb2gmx command  I am getting the following
error :-

Library file FF.dat not found in current dir nor in default directories...
how to rectify this ??

-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com
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Re: [gmx-users] links warnangles

[vferrario]

Thanks a lot!!!

Valerio


"Justin A. Lemkul"  ha scritto:




Justin A. Lemkul wrote:



I've obtained a stable trajectory for a single CHCL3 molecule.  By  
setting "continuation = no" (so that constraints are not solved  
before step 0) in the em.mdp file, and then reducing nstlist to 5  
in md.mdp, I


Ack, this should be "continuation = yes."  Sorry for the confusion.   
I will copy from my .mdp file...I will copy from my .mdp file... :)


-Justin

--


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] links warnangles

[vferrario]

Just the last thing... can you copy your mdp file? I think I'm having  
some problems also with that... Thanks.


Valerio


"Justin A. Lemkul"  ha scritto:




Justin A. Lemkul wrote:



I've obtained a stable trajectory for a single CHCL3 molecule.  By  
setting "continuation = no" (so that constraints are not solved  
before step 0) in the em.mdp file, and then reducing nstlist to 5  
in md.mdp, I


Ack, this should be "continuation = yes."  Sorry for the confusion.   
I will copy from my .mdp file...I will copy from my .mdp file... :)


-Justin

--


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] links warnangles

[Justin A. Lemkul]

vferra...@units.it wrote:
Just the last thing... can you copy your mdp file? I think I'm having 
some problems also with that... Thanks.




For EM, I used the .mdp file you posted in your first message and added the line 
"continuation = yes."  For MD, I changed nstlist from 100 to 5.


-Justin


Valerio


"Justin A. Lemkul"  ha scritto:




Justin A. Lemkul wrote:



I've obtained a stable trajectory for a single CHCL3 molecule.  By 
setting "continuation = no" (so that constraints are not solved 
before step 0) in the em.mdp file, and then reducing nstlist to 5 in 
md.mdp, I


Ack, this should be "continuation = yes."  Sorry for the confusion.  I 
will copy from my .mdp file...I will copy from my .mdp file... :)


-Justin

--


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] links warnangles

[vferrario]

Ok and which definition have you used? the previous one with 5 atom  
for molecule?


"Justin A. Lemkul"  ha scritto:




vferra...@units.it wrote:
Just the last thing... can you copy your mdp file? I think I'm  
having some problems also with that... Thanks.




For EM, I used the .mdp file you posted in your first message and  
added the line "continuation = yes."  For MD, I changed nstlist from  
100 to 5.


-Justin


Valerio


"Justin A. Lemkul"  ha scritto:




Justin A. Lemkul wrote:



I've obtained a stable trajectory for a single CHCL3 molecule.   
By setting "continuation = no" (so that constraints are not  
solved before step 0) in the em.mdp file, and then reducing  
nstlist to 5 in md.mdp, I


Ack, this should be "continuation = yes."  Sorry for the  
confusion.  I will copy from my .mdp file...I will copy from my  
.mdp file... :)


-Justin

--


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] links warnangles

[Justin A. Lemkul]

vferra...@units.it wrote:
Ok and which definition have you used? the previous one with 5 atom for 
molecule?




Yes.

-Justin


"Justin A. Lemkul"  ha scritto:




vferra...@units.it wrote:
Just the last thing... can you copy your mdp file? I think I'm having 
some problems also with that... Thanks.




For EM, I used the .mdp file you posted in your first message and 
added the line "continuation = yes."  For MD, I changed nstlist from 
100 to 5.


-Justin


Valerio


"Justin A. Lemkul"  ha scritto:




Justin A. Lemkul wrote:



I've obtained a stable trajectory for a single CHCL3 molecule.  By 
setting "continuation = no" (so that constraints are not solved 
before step 0) in the em.mdp file, and then reducing nstlist to 5 
in md.mdp, I


Ack, this should be "continuation = yes."  Sorry for the confusion.  
I will copy from my .mdp file...I will copy from my .mdp file... :)


-Justin

--


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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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] links warnangles

[vferrario]

The dynamic works, but I still have the same problems with minimization...


"Justin A. Lemkul"  ha scritto:




vferra...@units.it wrote:
Ok and which definition have you used? the previous one with 5 atom  
for molecule?




Yes.

-Justin


"Justin A. Lemkul"  ha scritto:




vferra...@units.it wrote:
Just the last thing... can you copy your mdp file? I think I'm  
having some problems also with that... Thanks.




For EM, I used the .mdp file you posted in your first message and  
added the line "continuation = yes."  For MD, I changed nstlist  
from 100 to 5.


-Justin


Valerio


"Justin A. Lemkul"  ha scritto:




Justin A. Lemkul wrote:



I've obtained a stable trajectory for a single CHCL3 molecule.   
By setting "continuation = no" (so that constraints are not  
solved before step 0) in the em.mdp file, and then reducing  
nstlist to 5 in md.mdp, I


Ack, this should be "continuation = yes."  Sorry for the  
confusion.  I will copy from my .mdp file...I will copy from my  
.mdp file... :)


-Justin

--


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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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] links warnangles

[Dimitris Dellis]

Hi.
There is an issue with constraints.
H atom position is not uniquely defined with the constraints you use.
Try these constraints (substitute symbols with numbers)

1   21   rC-H
1   31   rC-CL
1   41   rC-CL
1   51   rC-CL
2   31   rH-CL
2   41   rH-CL
3   41   rCL-CL
3   51   rCL-CL
4   51   rCL-CL

DD


On 02/02/2011 06:20 PM, vferra...@units.it wrote:
The dynamic works, but I still have the same problems with 
minimization...



"Justin A. Lemkul"  ha scritto:




vferra...@units.it wrote:
Ok and which definition have you used? the previous one with 5 atom 
for molecule?




Yes.

-Justin


"Justin A. Lemkul"  ha scritto:




vferra...@units.it wrote:
Just the last thing... can you copy your mdp file? I think I'm 
having some problems also with that... Thanks.




For EM, I used the .mdp file you posted in your first message and 
added the line "continuation = yes."  For MD, I changed nstlist 
from 100 to 5.


-Justin


Valerio


"Justin A. Lemkul"  ha scritto:




Justin A. Lemkul wrote:



I've obtained a stable trajectory for a single CHCL3 molecule.  
By setting "continuation = no" (so that constraints are not 
solved before step 0) in the em.mdp file, and then reducing 
nstlist to 5 in md.mdp, I


Ack, this should be "continuation = yes."  Sorry for the 
confusion.  I will copy from my .mdp file...I will copy from my 
.mdp file... :)


-Justin

--


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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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] protein+ligand+membrane: which forcefield?

[anna . marabotti]

Dear all,

I have to perform a simulation in which a protein with a ligand is
included in a lipid bilayer+water. In the Justin Lemkul's tutorial on
membrane simulations, I see that the chosen forcefield is Gromos96 53a6
manually corrected to include the Berger lipids parameters. However, to
create the topology of the ligand, I usually use PRODRG that produces
the topology and parameters using the Gromos96 43a1 forcefield (it
should do, at least...I see that the web server has recently changed and
I don't see the indication of the forcefield used inside...) My
question is: how to deal with the two different forcefields? I see in
the gmx-user list that the use of different forcefields is strongly
discouraged (and I agree with this suggestion) however if I have to
manage such different systems, what can I do? Can I add the Berger
lipids parameters to Gromos96 43a1 and use this corrected forcefield
instead? I did not understand if the Gromos 53a6 ff was chosen in the
tutorial because it is better than 43a1 to manage such systems, or
because it is more compliant than 43a1 with Berger lipids parameters.

Many thanks for suggestions and best regards.

Anna Marabotti
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Re: [gmx-users] energy minimization of a charged system in vacuum

[devicerandom]

On 30/01/11 16:13, David van der Spoel wrote:

On 2011-01-30 17.08, ms wrote:

Since I have exactly the same needs (charged system in vacuum) I jump
in...

In http://www.gromacs.org/Documentation/Errors
it says:

Note for PME users: It is possible to use a uniform neutralizing
background charge in PME to compensate for a system with a net
background charge. There is probably nothing wrong with this in
principle, because the uniform charge will not perturb the dynamics.


I'd like to comment that, this is tricky business. If your charges are
spread out homogeneously it may be OK, but in practice this is often not
the case (e.g. side chains on a protein). One should try to avoid this
if at all possible.


Oh, this is very bad news. Could you elaborate on that? (I have a CG
model where this would be badly needed).

With homogeneous I mean a solution of ions.


Hmm, I would be happy to have more informations -that is, *why* should 
one try to avoid this? What artefacts/problems should I expect?


Here:
http://bit.ly/ig11UQ

it seems that people use PME -with CHARMM here- to model efficiently 
non-neutral systems:


"As a result of including only the ion of interest in our simulations, 
the system will have a non-neutral charge. With particle-mesh Ewald 
electrostatics, this will result in a uniform neutralizing plasma [29] 
and [30]. In other words, a homogeneous neutralizing background charge 
is implicitly applied to the entire simulation space to avoid the 
divergence of the Ewald sum and to neutralize the system [29] and [30]. 
Although the background charge will alter the free energy profile, its 
effect can be shown to be negligible for a non-neutral charge of 2 e. 
The offset of the electrostatic free energy can be determined from [30] 
M.A. Kastenholz and P.H. Hünenberger, J. Phys. Chem. B 108 (2004), p. 
774. Full Text via CrossRef | View Record in Scopus | Cited By in Scopus 
(58)[30]"


Of course they may be horribly wrong, but they list some literature in 
support (which I'm going to check, but meanwhile...)



Can spreading neutralizing charges along the other chain atoms be a
viable alternative for enough atoms and enough low charge? (e.g. if I
have 100 atoms and a +5 net charge, adding a -0.05 charge on all others?)


Sounds like a recipe for disaster.


Uhm, given that mine is already a coarse-grained systems where 
practically all particles have 0 charge it could indeed change things 
badly. I've read this idea on one of the links of the mailing lists 
linked above in the thread.



Try looking for solutions with
explicit counter ions.


That's exactly the point: I desperately need to *avoid* explicit counter 
ions. I don't want interactions between my systems and "fake" counterions.


Thanks a lot,
Massimo
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Re: [gmx-users] links warnangles

[Justin A. Lemkul]

Dimitris Dellis wrote:

Hi.
There is an issue with constraints.
H atom position is not uniquely defined with the constraints you use.
Try these constraints (substitute symbols with numbers)

1   21   rC-H
1   31   rC-CL
1   41   rC-CL
1   51   rC-CL
2   31   rH-CL
2   41   rH-CL
3   41   rCL-CL
3   51   rCL-CL 
4   51   rCL-CL 



I suggested this solution long ago, but Berk said it was an incorrect approach:

http://redmine.gromacs.org/issues/359

-Justin


DD


On 02/02/2011 06:20 PM, vferra...@units.it wrote:
The dynamic works, but I still have the same problems with 
minimization...



"Justin A. Lemkul"  ha scritto:




vferra...@units.it wrote:
Ok and which definition have you used? the previous one with 5 atom 
for molecule?




Yes.

-Justin


"Justin A. Lemkul"  ha scritto:




vferra...@units.it wrote:
Just the last thing... can you copy your mdp file? I think I'm 
having some problems also with that... Thanks.




For EM, I used the .mdp file you posted in your first message and 
added the line "continuation = yes."  For MD, I changed nstlist 
from 100 to 5.


-Justin


Valerio


"Justin A. Lemkul"  ha scritto:




Justin A. Lemkul wrote:



I've obtained a stable trajectory for a single CHCL3 molecule.  
By setting "continuation = no" (so that constraints are not 
solved before step 0) in the em.mdp file, and then reducing 
nstlist to 5 in md.mdp, I


Ack, this should be "continuation = yes."  Sorry for the 
confusion.  I will copy from my .mdp file...I will copy from my 
.mdp file... :)


-Justin

--


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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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] energy minimization of a charged system in vacuum

[devicerandom]

On 30/01/11 16:13, David van der Spoel wrote:

On 2011-01-30 17.08, ms wrote:

On 30/01/11 15:41, David van der Spoel wrote:

Since I have exactly the same needs (charged system in vacuum) I jump
in...

In http://www.gromacs.org/Documentation/Errors
it says:

Note for PME users: It is possible to use a uniform neutralizing
background charge in PME to compensate for a system with a net
background charge. There is probably nothing wrong with this in
principle, because the uniform charge will not perturb the dynamics.


I'd like to comment that, this is tricky business. If your charges are
spread out homogeneously it may be OK, but in practice this is often not
the case (e.g. side chains on a protein). One should try to avoid this
if at all possible.


Oh, this is very bad news. Could you elaborate on that? (I have a CG
model where this would be badly needed).


Further info I found with a lazy check on gscholar:

http://bit.ly/hzzvEx

"Although the stability of a trajectory is a necessary condition for 
studying equilibrium observables of a molecular system, it is not a 
sufficient one to guarantee their correctness. The use of lattice 
summation methods implies that periodicity in a system simulated under 
periodic boundary conditions is considered to be an intrinsic property 
of this system. We refer to this choice as Ewald boundary conditions 
(EWBC). There are a number of reasons to expect that the use of EWBC for 
simulating solutions may lead to undesirable side effects. [...] 
Finally, when a non-neutral solute is considered, the use of EWBC 
implicitly introduces a homogeneous background charge that neutralizes 
the unit cell. This charge density will not model realistically the 
charge density arising from a counter-ion atmosphere, because (i) it 
overlaps with solute atoms; (ii) it is independent of the distance to 
the surface of the solute molecule; and (iii) it completely neutralizes 
the solute charge within an arbitrary volume of solution, the volume of 
the unit cell."


I would love to know how the way GROMACS does PME compares with this...

thanks!
m.
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Re: [gmx-users] protein+ligand+membrane: which forcefield?

[Justin A. Lemkul]

anna.marabo...@isa.cnr.it wrote:

Dear all,

I have to perform a simulation in which a protein with a ligand is
included in a lipid bilayer+water. In the Justin Lemkul's tutorial on
membrane simulations, I see that the chosen forcefield is Gromos96 53a6
manually corrected to include the Berger lipids parameters. However, to
create the topology of the ligand, I usually use PRODRG that produces
the topology and parameters using the Gromos96 43a1 forcefield (it
should do, at least...I see that the web server has recently changed and
I don't see the indication of the forcefield used inside...) My


The original PRODRG produced topologies designed for use with Gromos87, but 
PRODRG beta includes 43A1:


http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta

Of course, neither is particularly accurate (see the linked paper):

http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips


question is: how to deal with the two different forcefields? I see in
the gmx-user list that the use of different forcefields is strongly
discouraged (and I agree with this suggestion) however if I have to
manage such different systems, what can I do? Can I add the Berger
lipids parameters to Gromos96 43a1 and use this corrected forcefield
instead? I did not understand if the Gromos 53a6 ff was chosen in the
tutorial because it is better than 43a1 to manage such systems, or
because it is more compliant than 43a1 with Berger lipids parameters.



I have seen both 43A1 and 53A6 used in conjunction with the Berger lipids, and 
there is no fundamental difference between the two with respect to membrane 
protein systems.  In fact, Berger + Gromos96 is, in and of itself, a compilation 
of different force fields.  It just happens that they play nicely with one 
another :)


I use 53A6 because it is newer and its derivation is published.  The information 
for 43A1 is not freely available (i.e., the GROMOS software manual), so I can't 
decide if I like it or not.  Thus, I generally do not use it.


As for your problem, since the PRODRG charges and charge groups are always 
incorrect (at least, I've never found a molecule it builds properly), you can 
replace them with whatever you choose.  Since the atom types (for most atoms) 
are named the same between 43A1 and 53A6, and the bonded parameters are the 
same, you can simply replace all of the charges and charge groups in the PRODRG 
topology and you will have a 53A6-compatible topology.  Of course, that implies 
you've derived those charges properly, which is no small task.


-Justin


Many thanks for suggestions and best regards.

Anna Marabotti


--


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] Improper dihedral

[Thomas Koller]

Hello!

I want to use improper type 4 in the top file, but this is not working. When I 
switch to type 2 everything is fine. What is the problem with type 4?

Regards,
Thomas
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Re: [gmx-users] mdrun with append option

[Sai Pooja]

The problem is solved with grompp i.e. I use the -t .cpt option. However,
now appending does not work. I remember Mark said in a previous mail that a
certain environment variable can allow appending to happen even in such
cases. I would liek to try that out.
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Re: [gmx-users] mdrun with append option

[Mark Abraham]

On 3/02/2011 6:15 AM, Sai Pooja wrote:
The problem is solved with grompp i.e. I use the -t .cpt option. 
However, now appending does not work. I remember Mark said in a 
previous mail that a certain environment variable can allow appending 
to happen even in such cases. I would liek to try that out.


No, I said that an environment variable can override the mechanism that 
blocks ensemble changes in mdrun.


Mark
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Re: [gmx-users] mdrun with append option

[Sai Pooja]

On Wed, Feb 2, 2011 at 3:15 PM, Mark Abraham wrote:

> On 3/02/2011 6:15 AM, Sai Pooja wrote:
>
>> The problem is solved with grompp i.e. I use the -t .cpt option. However,
>> now appending does not work. I remember Mark said in a previous mail that a
>> certain environment variable can allow appending to happen even in such
>> cases. I would liek to try that out.
>>
>> No, I said that an environment variable can override the mechanism that
> blocks ensemble changes in mdrun.
>

So how can I use this environment variable.. I might be asking an absurd
question since I don't really understand what an environment variable is.
But I would definitely liek to experiment with it, since I am in the process
of trying out these different options and figuring out which would be the
best.

I also need to understand something. What exactly does the tpbconv do when
only -s and -nsteps or -extend options are supplied - it seems that it takes
all the information(mass, topology, restraints) from the previous tpr file
and just changes the init_step parameter and the number of steps till which
the simulation should run.

Now if that is the case, I am still unable to understand that if the cpt
file is NOT provided to mdrun (or a mismatched one is provided), how does
mdrun obtain the coordinates, velocities, box-dimensions of the last frame.
If it doesn't use the ones of the last frame, what does it really use?

If it gets them from the new_tpr file, and the new_tpr file gets it from
previous_tpr file via tpbconv, then how does that ensure continuation from
the last frame, because the previous_tpr file might have been compiled even
before the simulation started. And as far as I know, it is purely an input
file to mdrun and has no information on the last coordinates/velocities of
the mdrun.

You may have answered this before but I have tried and failed in
understanding. I would request you to help me in understanding the above. I
would really appreciate it.

Regards
Pooja
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Re: [gmx-users] mdrun with append option

[Justin A. Lemkul]

Sai Pooja wrote:
 
On Wed, Feb 2, 2011 at 3:15 PM, Mark Abraham > wrote:


On 3/02/2011 6:15 AM, Sai Pooja wrote:

The problem is solved with grompp i.e. I use the -t .cpt option.
However, now appending does not work. I remember Mark said in a
previous mail that a certain environment variable can allow
appending to happen even in such cases. I would liek to try that
out.

No, I said that an environment variable can override the mechanism
that blocks ensemble changes in mdrun.

 
So how can I use this environment variable.. I might be asking an absurd 
question since I don't really understand what an environment variable 
is. But I would definitely liek to experiment with it, since I am in the 
process of trying out these different options and figuring out which 
would be the best.
 


http://en.wikipedia.org/wiki/Environment_variable

I think the pertinent one in this case is GMX_ALLOW_CPT_MISMATCH.  There is a 
reason these aren't well-documented; they probably shouldn't be used in most 
cases.  You should have seen a very specific error message in your .log file or 
screen output indicating that this situation was relevant 
(src/gmxlib/checkpoint.c, around line 1606).


I also need to understand something. What exactly does the tpbconv do 
when only -s and -nsteps or -extend options are supplied - it seems that 
it takes all the information(mass, topology, restraints) from the 
previous tpr file and just changes the init_step parameter and the 
number of steps till which the simulation should run.
 


All it does is modify the number of steps specified in the input file; init_step 
should be untouched.  The step from which the simulation is continued is in the 
.cpt file.


Now if that is the case, I am still unable to understand that if the cpt 
file is NOT provided to mdrun (or a mismatched one is provided), how 
does mdrun obtain the coordinates, velocities, box-dimensions of the 
last frame. If it doesn't use the ones of the last frame, what does it 
really use?
 


These are two cases.  If (1) an invalid .cpt file is provided, the simulation 
should stop with a fatal error (in checkpoint.c, described above); if (2) a 
checkpoint is not provided at all, then a completely new simulation is started, 
and the "last frame" is non-existent.  The simulation begins at time zero.


If it gets them from the new_tpr file, and the new_tpr file gets it from 
previous_tpr file via tpbconv, then how does that ensure continuation 
from the last frame, because the previous_tpr file might have been 
compiled even before the simulation started. And as far as I know, it is 
purely an input file to mdrun and has no information on the last 
coordinates/velocities of the mdrun.


If you provide a .tpr file to mdrun and the checkpoint file is invalid, the 
simulation should have stopped, per the fatal error given in checkpoint.c 
(described above).  The contents of your .log file should make clear exactly 
what mdrun is doing and where it's starting.


In the case you describe, "new.tpr" and "previous.tpr" differ only in the number 
of steps, therefore the state contained therein corresponds to the beginning of 
the simulation, i.e. time zero.


-Justin

 
You may have answered this before but I have tried and failed in 
understanding. I would request you to help me in understanding the 
above. I would really appreciate it.
 
Regards

Pooja



--


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] links warnangles

[Dimitris Dellis]

On 02/02/2011 07:47 PM, Justin A. Lemkul wrote:



Dimitris Dellis wrote:

Hi.
There is an issue with constraints.
H atom position is not uniquely defined with the constraints you use.
Try these constraints (substitute symbols with numbers)

1   21   rC-H
1   31   rC-CL
1   41   rC-CL
1   51   rC-CL
2   31   rH-CL
2   41   rH-CL
3   41   rCL-CL
3   51   rCL-CL 4   51   rCL-CL


I suggested this solution long ago, but Berk said it was an incorrect 
approach:


http://redmine.gromacs.org/issues/359



In the above suggestion, the number of constraints is 9, as it should be.
One constraint replaced by another in order to keep H position 
definition unique.

Over-constraining gives wrong results.

DD



-Justin


DD


On 02/02/2011 06:20 PM, vferra...@units.it wrote:
The dynamic works, but I still have the same problems with 
minimization...



"Justin A. Lemkul"  ha scritto:




vferra...@units.it wrote:
Ok and which definition have you used? the previous one with 5 
atom for molecule?




Yes.

-Justin


"Justin A. Lemkul"  ha scritto:




vferra...@units.it wrote:
Just the last thing... can you copy your mdp file? I think I'm 
having some problems also with that... Thanks.




For EM, I used the .mdp file you posted in your first message and 
added the line "continuation = yes."  For MD, I changed nstlist 
from 100 to 5.


-Justin


Valerio


"Justin A. Lemkul"  ha scritto:




Justin A. Lemkul wrote:



I've obtained a stable trajectory for a single CHCL3 
molecule.  By setting "continuation = no" (so that constraints 
are not solved before step 0) in the em.mdp file, and then 
reducing nstlist to 5 in md.mdp, I


Ack, this should be "continuation = yes."  Sorry for the 
confusion.  I will copy from my .mdp file...I will copy from my 
.mdp file... :)


-Justin

--


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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--


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] mdrun with append option

[Sai Pooja]

Thanks Justin for being so patient. I have understood almost everything and
I hope this is the last question on this thread.

See inline ...
On Wed, Feb 2, 2011 at 5:53 PM, Justin A. Lemkul  wrote:

>
>
> Sai Pooja wrote:
>
>  On Wed, Feb 2, 2011 at 3:15 PM, Mark Abraham > mark.abra...@anu.edu.au>> wrote:
>>
>>On 3/02/2011 6:15 AM, Sai Pooja wrote:
>>
>>The problem is solved with grompp i.e. I use the -t .cpt option.
>>However, now appending does not work. I remember Mark said in a
>>previous mail that a certain environment variable can allow
>>appending to happen even in such cases. I would liek to try that
>>out.
>>
>>No, I said that an environment variable can override the mechanism
>>that blocks ensemble changes in mdrun.
>>
>>  So how can I use this environment variable.. I might be asking an absurd
>> question since I don't really understand what an environment variable is.
>> But I would definitely liek to experiment with it, since I am in the process
>> of trying out these different options and figuring out which would be the
>> best.
>>
>>
>
> http://en.wikipedia.org/wiki/Environment_variable
>
> I think the pertinent one in this case is GMX_ALLOW_CPT_MISMATCH.  There is
> a reason these aren't well-documented; they probably shouldn't be used in
> most cases.  You should have seen a very specific error message in your .log
> file or screen output indicating that this situation was relevant
> (src/gmxlib/checkpoint.c, around line 1606).
>
>
> I also need to understand something. What exactly does the tpbconv do when
>> only -s and -nsteps or -extend options are supplied - it seems that it takes
>> all the information(mass, topology, restraints) from the previous tpr file
>> and just changes the init_step parameter and the number of steps till which
>> the simulation should run.
>>
>>
>
> All it does is modify the number of steps specified in the input file;
> init_step should be untouched.  The step from which the simulation is
> continued is in the .cpt file.
>
>
> Now if that is the case, I am still unable to understand that if the cpt
>> file is NOT provided to mdrun (or a mismatched one is provided), how does
>> mdrun obtain the coordinates, velocities, box-dimensions of the last frame.
>> If it doesn't use the ones of the last frame, what does it really use?
>>
>>
>
> These are two cases.  If (1) an invalid .cpt file is provided, the
> simulation should stop with a fatal error (in checkpoint.c, described
> above); if (2) a checkpoint is not provided at all, then a completely new
> simulation is started, and the "last frame" is non-existent.  The simulation
> begins at time zero.
>
>
> If it gets them from the new_tpr file, and the new_tpr file gets it from
>> previous_tpr file via tpbconv, then how does that ensure continuation from
>> the last frame, because the previous_tpr file might have been compiled even
>> before the simulation started. And as far as I know, it is purely an input
>> file to mdrun and has no information on the last coordinates/velocities of
>> the mdrun.
>>
>
> If you provide a .tpr file to mdrun and the checkpoint file is invalid, the
> simulation should have stopped, per the fatal error given in checkpoint.c
> (described above).  The contents of your .log file should make clear exactly
> what mdrun is doing and where it's starting.
>


In my case, I use tpbconv with just nsteps and old_tpr and supply the
exchanged .cpt file. Mdrun does not crash, but none of the files get
appended. All files start from the first continuation step. The logfile has
no error. Same is the case with the #rexlog0.log# file which is the logfile
which gets overwritten. I don't know what conclusion to draw - would it make
sense to compare the last frame in the .cpt file and the first frame in the
new xtc file? Should they match if the cpt file has infact been used by
mdrun?

Pooja


>
> In the case you describe, "new.tpr" and "previous.tpr" differ only in the
> number of steps, therefore the state contained therein corresponds to the
> beginning of the simulation, i.e. time zero.
>
> -Justin
>
>
>  You may have answered this before but I have tried and failed in
>> understanding. I would request you to help me in understanding the above. I
>> would really appreciate it.
>>  Regards
>> Pooja
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
>  gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ..

Re: [gmx-users] mdrun with append option

[Sai Pooja]

On Wed, Feb 2, 2011 at 6:49 PM, Sai Pooja  wrote:

> Thanks Justin for being so patient. I have understood almost everything and
> I hope this is the last question on this thread.
>
> See inline ...
>  On Wed, Feb 2, 2011 at 5:53 PM, Justin A. Lemkul  wrote:
>
>>
>>
>> Sai Pooja wrote:
>>
>>  On Wed, Feb 2, 2011 at 3:15 PM, Mark Abraham 
>> >> mark.abra...@anu.edu.au>> wrote:
>>>
>>>On 3/02/2011 6:15 AM, Sai Pooja wrote:
>>>
>>>The problem is solved with grompp i.e. I use the -t .cpt option.
>>>However, now appending does not work. I remember Mark said in a
>>>previous mail that a certain environment variable can allow
>>>appending to happen even in such cases. I would liek to try that
>>>out.
>>>
>>>No, I said that an environment variable can override the mechanism
>>>that blocks ensemble changes in mdrun.
>>>
>>>  So how can I use this environment variable.. I might be asking an absurd
>>> question since I don't really understand what an environment variable is.
>>> But I would definitely liek to experiment with it, since I am in the process
>>> of trying out these different options and figuring out which would be the
>>> best.
>>>
>>>
>>
>> http://en.wikipedia.org/wiki/Environment_variable
>>
>> I think the pertinent one in this case is GMX_ALLOW_CPT_MISMATCH.  There
>> is a reason these aren't well-documented; they probably shouldn't be used in
>> most cases.  You should have seen a very specific error message in your .log
>> file or screen output indicating that this situation was relevant
>> (src/gmxlib/checkpoint.c, around line 1606).
>>
>>
>> I also need to understand something. What exactly does the tpbconv do when
>>> only -s and -nsteps or -extend options are supplied - it seems that it takes
>>> all the information(mass, topology, restraints) from the previous tpr file
>>> and just changes the init_step parameter and the number of steps till which
>>> the simulation should run.
>>>
>>>
>>
>> All it does is modify the number of steps specified in the input file;
>> init_step should be untouched.  The step from which the simulation is
>> continued is in the .cpt file.
>>
>>
>> Now if that is the case, I am still unable to understand that if the cpt
>>> file is NOT provided to mdrun (or a mismatched one is provided), how does
>>> mdrun obtain the coordinates, velocities, box-dimensions of the last frame.
>>> If it doesn't use the ones of the last frame, what does it really use?
>>>
>>>
>>
>> These are two cases.  If (1) an invalid .cpt file is provided, the
>> simulation should stop with a fatal error (in checkpoint.c, described
>> above); if (2) a checkpoint is not provided at all, then a completely new
>> simulation is started, and the "last frame" is non-existent.  The simulation
>> begins at time zero.
>>
>>
>> If it gets them from the new_tpr file, and the new_tpr file gets it from
>>> previous_tpr file via tpbconv, then how does that ensure continuation from
>>> the last frame, because the previous_tpr file might have been compiled even
>>> before the simulation started. And as far as I know, it is purely an input
>>> file to mdrun and has no information on the last coordinates/velocities of
>>> the mdrun.
>>>
>>
>> If you provide a .tpr file to mdrun and the checkpoint file is invalid,
>> the simulation should have stopped, per the fatal error given in
>> checkpoint.c (described above).  The contents of your .log file should make
>> clear exactly what mdrun is doing and where it's starting.
>>
>
They do infact match! So mdrun starts from the checkpoint file provided!
Files do not get appended but runs are in continuation.

Thanks!
Pooja

>
>
> In my case, I use tpbconv with just nsteps and old_tpr and supply the
> exchanged .cpt file. Mdrun does not crash, but none of the files get
> appended. All files start from the first continuation step. The logfile has
> no error. Same is the case with the #rexlog0.log# file which is the logfile
> which gets overwritten. I don't know what conclusion to draw - would it make
> sense to compare the last frame in the .cpt file and the first frame in the
> new xtc file? Should they match if the cpt file has infact been used by
> mdrun?
>
> Pooja
>
>
>>
>> In the case you describe, "new.tpr" and "previous.tpr" differ only in the
>> number of steps, therefore the state contained therein corresponds to the
>> beginning of the simulation, i.e. time zero.
>>
>> -Justin
>>
>>
>>  You may have answered this before but I have tried and failed in
>>> understanding. I would request you to help me in understanding the above. I
>>> would really appreciate it.
>>>  Regards
>>> Pooja
>>>
>>>
>> --
>> 
>>
>> 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
>>
>> ==

Re: [gmx-users] mdrun with append option

[Justin A. Lemkul]

Sai Pooja wrote:
Thanks Justin for being so patient. I have understood almost everything 
and I hope this is the last question on this thread.
 
See inline ...
On Wed, Feb 2, 2011 at 5:53 PM, Justin A. Lemkul > wrote:




Sai Pooja wrote:

 On Wed, Feb 2, 2011 at 3:15 PM, Mark Abraham
mailto:mark.abra...@anu.edu.au>
>> wrote:

   On 3/02/2011 6:15 AM, Sai Pooja wrote:

   The problem is solved with grompp i.e. I use the -t .cpt
option.
   However, now appending does not work. I remember Mark
said in a
   previous mail that a certain environment variable can allow
   appending to happen even in such cases. I would liek to
try that
   out.

   No, I said that an environment variable can override the
mechanism
   that blocks ensemble changes in mdrun.

 So how can I use this environment variable.. I might be asking
an absurd question since I don't really understand what an
environment variable is. But I would definitely liek to
experiment with it, since I am in the process of trying out
these different options and figuring out which would be the best.
 



http://en.wikipedia.org/wiki/Environment_variable

I think the pertinent one in this case is GMX_ALLOW_CPT_MISMATCH.
 There is a reason these aren't well-documented; they probably
shouldn't be used in most cases.  You should have seen a very
specific error message in your .log file or screen output indicating
that this situation was relevant (src/gmxlib/checkpoint.c, around
line 1606).


I also need to understand something. What exactly does the
tpbconv do when only -s and -nsteps or -extend options are
supplied - it seems that it takes all the information(mass,
topology, restraints) from the previous tpr file and just
changes the init_step parameter and the number of steps till
which the simulation should run.
 



All it does is modify the number of steps specified in the input
file; init_step should be untouched.  The step from which the
simulation is continued is in the .cpt file.


Now if that is the case, I am still unable to understand that if
the cpt file is NOT provided to mdrun (or a mismatched one is
provided), how does mdrun obtain the coordinates, velocities,
box-dimensions of the last frame. If it doesn't use the ones of
the last frame, what does it really use?
 



These are two cases.  If (1) an invalid .cpt file is provided, the
simulation should stop with a fatal error (in checkpoint.c,
described above); if (2) a checkpoint is not provided at all, then a
completely new simulation is started, and the "last frame" is
non-existent.  The simulation begins at time zero.


If it gets them from the new_tpr file, and the new_tpr file gets
it from previous_tpr file via tpbconv, then how does that ensure
continuation from the last frame, because the previous_tpr file
might have been compiled even before the simulation started. And
as far as I know, it is purely an input file to mdrun and has no
information on the last coordinates/velocities of the mdrun.


If you provide a .tpr file to mdrun and the checkpoint file is
invalid, the simulation should have stopped, per the fatal error
given in checkpoint.c (described above).  The contents of your .log
file should make clear exactly what mdrun is doing and where it's
starting.

 
 
In my case, I use tpbconv with just nsteps and old_tpr and supply the 
exchanged .cpt file. Mdrun does not crash, but none of the files get 
appended. All files start from the first continuation step. The logfile 
has no error. Same is the case with the #rexlog0.log# file which is the 
logfile which gets overwritten. I don't know what conclusion to draw - 
would it make sense to compare the last frame in the .cpt file and the 
first frame in the new xtc file? Should they match if the cpt file has 
infact been used by mdrun?
 


If the frames correspond to the same point in time, the coordinates, etc should 
be the same.  This is certainly easy enough to test in a few seconds.


-Justin


Pooja
 



In the case you describe, "new.tpr" and "previous.tpr" differ only
in the number of steps, therefore the state contained therein
corresponds to the beginning of the simulation, i.e. time zero.

-Justin


 You may have answered this before but I have tried and failed
in understanding. I would request you to help me in
understanding the above. I would really appreciate it.
 Regards
Pooja


-- 



Justin A. Lemkul