[gmx-users] Distance travelled from time 0
Hi guys, What is the best way of calculating how far a residue has traveled from its starting position during a simulations? Thanks Natalie -- 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
[gmx-users] FW: Myristic Acid Simulations
Hi, I know there have been many threads talking about parameterization of novel molecules for simulations within gromacs, but I just wanted to know if anyone had done any parameterization of myristic acid, as I intend to begin simulations on a protein that is myristolated and figured I'd check here before embarking on what sounds like it will be a very long and confusing process for a parameterization-newbie. I found a paper in which they've used myristic acid within their simulations (Ariel Alvarez et al., 2012, J.Biophys. http://www.hindawi.com/journals/jbp/2012/642745/) however they've only listed the topology coordinates of this molecule. Is it possible to create a .rtp from this topology? Would this require parameterization based on the force field I am using? If so where would I find information on the bond angles and dihedrals for this? Any advice on creating a .rtp file would be greatly appreciated!! Thanks Natalie -- 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] Potential Energy Landscape
Thanks I'll give PCA a try! Natalie From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Mark Abraham [mark.abra...@anu.edu.au] Sent: 21 November 2011 12:04 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Potential Energy Landscape On 21/11/2011 10:36 PM, Natalie Stephenson wrote: > I have performed force pulling experiments on a protein with both Gromacs MD > simulations and experimentally with AFM. The problem I'm facing with the > data is the difference between the loading rates of the two approaches. For > the MDS the loading rate is around 10 N/s, whereas the AFM experiments have a > much lower loading rate of 1 x 10^-8 N/s. > > I was told at a conference I attended that there was a way of constructing a > 'potential energy landscape' which would be able to use this to remove the > loading rate differences. However, I did not get a chance to find out how > this was possible. I understand how g_sham works, however, I'm not sure what > - in this case - the input would be in order to construct such a 'potential > energy landscape'. Any insight into how I would be able to create this ... or > any other ideas on how I would be able to somehow relate the simulation > output to experimental data dispite the loading rate differences would be > GREATLY appreciated!! Forget the misleading term "potential energy landscape". It seems nobody here knows how your contact thinks constructing a plot of free energy as a function of two observables will address the loading rate difference. Justin described how g_sham works. Your analysis may suggest the right observables for use with g_sham, or you may wish to use essential dynamics (aka principal component analysis) to determine these algorithmically. Check out manual 8.10 if so. Mark > > Thanks once again!! > Natalie > > > Natalie Stephenson, B.Sc > PhD Research Associate > > Manchester Interdisciplinary Biocentre > 131 Princess Street > Manchester > M1 7DN > x65816 > > > ____ > From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf > of Natalie Stephenson [natalie.stephen...@postgrad.manchester.ac.uk] > Sent: 14 November 2011 12:15 > To: jalem...@vt.edu; Discussion list for GROMACS users > Subject: RE: [gmx-users] Potential Energy Landscape > > > From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf > of Justin A. Lemkul [jalem...@vt.edu] > Sent: 21 October 2011 13:25 > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] Potential Energy Landscape > > Natalie Stephenson wrote: >>> Hi Justin (and gmx-users), >>> >>> I've been looking into using g_sham for the free energy landscapes, however >>> I'm not sure what variables I should plot ... could I just use the g_energy >>> (potential) outputs to produce the energy landscape?? Other examples I've >>> seen using g_sham have done quite in depth eigenvector projections before >>> plotting them using g_sham. >>> >> The free energy of potential energy is probably not a meaningful quantity ;) >> >>> What inputs would I require in order to determine how loading rate an >>> increased loading rate on the simulation would change the force results? >>> >>> I know I'm probably being completely dumb but my use of maths has been >>> sporadic to say the least in the last 7 years ... so getting back into it is >>> proving more confusing! >>> >> You haven't provided a lot of detail about what you're doing, what you've >> measured, or what you hope to achieve. In general, one plots two variables >> (one >> on each axis), and g_sham calculates a free energy based simply on the >> probability of occurrence of these values. For instance, for protein folding >> experiments, often the RMSD relative to the known structure is one variable, >> and >> something else like native contacts or hydrogen bonds is plotted as the other >> variable. The free energy surface is then generated as a function of >> intramolecular association and similarity to a known structure. >> >> -Justin >> > Sorry it's taken so long to reply to this one, experimental issues dragged my > focus! > I have performed force pulling experiments on a protein with both Gromacs MD > simulations and experimentally with AFM. The problem I'm facing with the > data is the d
RE: [gmx-users] Potential Energy Landscape
I have performed force pulling experiments on a protein with both Gromacs MD simulations and experimentally with AFM. The problem I'm facing with the data is the difference between the loading rates of the two approaches. For the MDS the loading rate is around 10 N/s, whereas the AFM experiments have a much lower loading rate of 1 x 10^-8 N/s. I was told at a conference I attended that there was a way of constructing a 'potential energy landscape' which would be able to use this to remove the loading rate differences. However, I did not get a chance to find out how this was possible. I understand how g_sham works, however, I'm not sure what - in this case - the input would be in order to construct such a 'potential energy landscape'. Any insight into how I would be able to create this ... or any other ideas on how I would be able to somehow relate the simulation output to experimental data dispite the loading rate differences would be GREATLY appreciated!! Thanks once again!! Natalie ------------ Natalie Stephenson, B.Sc PhD Research Associate Manchester Interdisciplinary Biocentre 131 Princess Street Manchester M1 7DN x65816 From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Natalie Stephenson [natalie.stephen...@postgrad.manchester.ac.uk] Sent: 14 November 2011 12:15 To: jalem...@vt.edu; Discussion list for GROMACS users Subject: RE: [gmx-users] Potential Energy Landscape From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: 21 October 2011 13:25 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Potential Energy Landscape Natalie Stephenson wrote: >> Hi Justin (and gmx-users), >> >> I've been looking into using g_sham for the free energy landscapes, however >> I'm not sure what variables I should plot ... could I just use the g_energy >> (potential) outputs to produce the energy landscape?? Other examples I've >> seen using g_sham have done quite in depth eigenvector projections before >> plotting them using g_sham. >> > >The free energy of potential energy is probably not a meaningful quantity ;) > >> What inputs would I require in order to determine how loading rate an >> increased loading rate on the simulation would change the force results? >> >> I know I'm probably being completely dumb but my use of maths has been >> sporadic to say the least in the last 7 years ... so getting back into it is >> proving more confusing! >> > >You haven't provided a lot of detail about what you're doing, what you've >measured, or what you hope to achieve. In general, one plots two variables >(one >on each axis), and g_sham calculates a free energy based simply on the >probability of occurrence of these values. For instance, for protein folding >experiments, often the RMSD relative to the known structure is one variable, >and >something else like native contacts or hydrogen bonds is plotted as the other >variable. The free energy surface is then generated as a function of >intramolecular association and similarity to a known structure. > >-Justin > Sorry it's taken so long to reply to this one, experimental issues dragged my focus! I have performed force pulling experiments on a protein with both Gromacs MD simulations and experimentally with AFM. The problem I'm facing with the data is the difference between the loading rates of the two approaches. For the MDS the loading rate is around 10 N/s, whereas the AFM experiments have a much lower loading rate of 1 x 10^-8 N/s. I was told at a conference I attended that there was a way of constructing a 'potential energy landscape' which would be able to use this to remove the loading rate differences. However, I did not get a chance to find out how this was possible. I understand how g_sham works, however, I'm not sure what - in this case - the input would be in order to construct such a 'potential energy landscape'. Any insight into how I would be able to create this ... or any other ideas on how I would be able to somehow relate the simulation output to experimental data dispite the loading rate differences would be GREATLY appreciated!! Thanks once again!! Natalie > Natalie > > Natalie Stephenson, B.Sc PhD > Research Associate > > Manchester Interdisciplinary Biocentre 131 Princess Street Manchester M1 7DN > x65816 > > ________ From: gmx-users-boun...@gro
RE: [gmx-users] Potential Energy Landscape
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: 21 October 2011 13:25 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Potential Energy Landscape Natalie Stephenson wrote: >> Hi Justin (and gmx-users), >> >> I've been looking into using g_sham for the free energy landscapes, however >> I'm not sure what variables I should plot ... could I just use the g_energy >> (potential) outputs to produce the energy landscape?? Other examples I've >> seen using g_sham have done quite in depth eigenvector projections before >> plotting them using g_sham. >> > >The free energy of potential energy is probably not a meaningful quantity ;) > >> What inputs would I require in order to determine how loading rate an >> increased loading rate on the simulation would change the force results? >> >> I know I'm probably being completely dumb but my use of maths has been >> sporadic to say the least in the last 7 years ... so getting back into it is >> proving more confusing! >> > >You haven't provided a lot of detail about what you're doing, what you've >measured, or what you hope to achieve. In general, one plots two variables >(one >on each axis), and g_sham calculates a free energy based simply on the >probability of occurrence of these values. For instance, for protein folding >experiments, often the RMSD relative to the known structure is one variable, >and >something else like native contacts or hydrogen bonds is plotted as the other >variable. The free energy surface is then generated as a function of >intramolecular association and similarity to a known structure. > >-Justin > Sorry it's taken so long to reply to this one, experimental issues dragged my focus! I have performed force pulling experiments on a protein with both Gromacs MD simulations and experimentally with AFM. The problem I'm facing with the data is the difference between the loading rates of the two approaches. For the MDS the loading rate is around 10 N/s, whereas the AFM experiments have a much lower loading rate of 1 x 10^-8 N/s. I was told at a conference I attended that there was a way of constructing a 'potential energy landscape' which would be able to use this to remove the loading rate differences. However, I did not get a chance to find out how this was possible. I understand how g_sham works, however, I'm not sure what - in this case - the input would be in order to construct such a 'potential energy landscape'. Any insight into how I would be able to create this ... or any other ideas on how I would be able to somehow relate the simulation output to experimental data dispite the loading rate differences would be GREATLY appreciated!! Thanks once again!! Natalie > Natalie > > Natalie Stephenson, B.Sc PhD > Research Associate > > Manchester Interdisciplinary Biocentre 131 Princess Street Manchester M1 7DN > x65816 > > From: gmx-users-boun...@gromacs.org > [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul > [jalem...@vt.edu] Sent: 12 October 2011 18:22 To: Discussion list for GROMACS > users Subject: Re: [gmx-users] Potential Energy Landscape > > Natalie Stephenson wrote: >> I was recently told in passing that it would be possible to construct a >> 'potential energy landscape' from the simulations I have performed. This >> way I could remove any loading rate differences between simulations and >> experimental force experiments I've been performing ... however I cannot >> find anywhere in which this is mentioned. >> >> The only thing close I could find that was close was the free energy >> landscape using g_anaeig under the Dihedral PCA >> (http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA?highlight=dihedral+pca >> >> <http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA?highlight=dihedral+pca>) >> however, I'm not sure this is what I'm looking for. >> >> Does anyone know where I would be able to find out / read more about how to >> create potential energy landscapes from my simulation outputs? >> > > g_sham produces free energy landscapes for any variables plotted against one > another. > > -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
RE: [gmx-users] Potential Energy Landscape
Hi Justin (and gmx-users), I've been looking into using g_sham for the free energy landscapes, however I'm not sure what variables I should plot ... could I just use the g_energy (potential) outputs to produce the energy landscape?? Other examples I've seen using g_sham have done quite in depth eigenvector projections before plotting them using g_sham. What inputs would I require in order to determine how loading rate an increased loading rate on the simulation would change the force results? I know I'm probably being completely dumb but my use of maths has been sporadic to say the least in the last 7 years ... so getting back into it is proving more confusing! Natalie -------- Natalie Stephenson, B.Sc PhD Research Associate Manchester Interdisciplinary Biocentre 131 Princess Street Manchester M1 7DN x65816 From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: 12 October 2011 18:22 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Potential Energy Landscape Natalie Stephenson wrote: > I was recently told in passing that it would be possible to construct a > 'potential energy landscape' from the simulations I have performed. > This way I could remove any loading rate differences between simulations > and experimental force experiments I've been performing ... however I > cannot find anywhere in which this is mentioned. > > The only thing close I could find that was close was the free energy > landscape using g_anaeig under the Dihedral PCA > (http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA?highlight=dihedral+pca > <http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA?highlight=dihedral+pca>) > however, I'm not sure this is what I'm looking for. > > Does anyone know where I would be able to find out / read more about how > to create potential energy landscapes from my simulation outputs? > g_sham produces free energy landscapes for any variables plotted against one another. -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 -- 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
[gmx-users] Potential Energy Landscape
I was recently told in passing that it would be possible to construct a 'potential energy landscape' from the simulations I have performed. This way I could remove any loading rate differences between simulations and experimental force experiments I've been performing ... however I cannot find anywhere in which this is mentioned. The only thing close I could find that was close was the free energy landscape using g_anaeig under the Dihedral PCA (http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA?highlight=dihedral+pca) however, I'm not sure this is what I'm looking for. Does anyone know where I would be able to find out / read more about how to create potential energy landscapes from my simulation outputs? Thanks Natalie -- 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
[gmx-users] quick question about "direction_periodic"
Hi guys, I was just wondering if with "direction_periodic" the pull simulations pulls at both ends of the protein rather than just one. I've previously been position restraining the C-terminus of my protein and pulling on the N-terminus. With the "distance" pull code this seems to do exactly that - hold the C- and pull the N- away from it. Changing over to the "direction_periodic" it seems that the force is being applied to both the C- and N- termini even though the position restraint file has been specified when creating the .tpr with grompp ... is this right? How can I stop it from pulling on both termini if this is in fact the case? Thanks Natalie -------- Natalie Stephenson, B.Sc PhD Research Associate Manchester Interdisciplinary Biocentre 131 Princess Street Manchester M1 7DN x65816 -- 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
[gmx-users] Pull Simulation: Force spike on F vs X output and extension stall
Hi, I was wondering if you would be able to clear up a slightly confusing aspect of the simulations I've been running. I am currently performing a pull simulation and when viewing the outputs of all the simulations I have run I see the extension of the protein stop when it reaches the same sub-domain each time (at around a 10 nm extension). The mdp file I use as the input file states that the pull distance should be much larger than this. Also when viewing the -px -pf outputs this agrees. When the simulation reaches a 10 nm extension it stops and only increases around 0.2 nm over the remaining simulation time (~3000 ps). When force extension is plotted there is still an increase in force which results in a spike at the 10 nm extension point, increasing the force from around 0.7 nN to around 30 nN. Is there any reason this could be an artefact or is it just the fact that this domain is very firmly in contact with it's adjacent domain? Thank you for your help with this matter. Kind regards, Natalie -------- Natalie Stephenson, B.Sc PhD Research Associate Manchester Interdisciplinary Biocentre 131 Princess Street Manchester M1 7DN x65816 -- 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] Specify run time
Thanks loads! That helps loads! Natalie Natalie Stephenson, B.Sc PhD Research Associate Manchester Interdisciplinary Biocentre 131 Princess Street Manchester M1 7DN x65816 From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Mark Abraham [mark.abra...@anu.edu.au] Sent: 20 May 2011 10:34 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Specify run time On 20/05/11, Natalie Stephenson wrote: Hi All, I was just wondering if anyone knew whether it was possible to tell Gromacs to run for a few hours, dump all the intermediate results and then exit. I was hoping to be able to use the checkpoint function to run the simulation for a bit, checkpoint it, exit then restart. Is this possible? GROMACS writes results progressively, so either choose a number of steps that will be suitable, or use mdrun -maxh. Then use the checkpoint to restart, per the restart instructions on the webpage Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Specify run time
Hi All, I was just wondering if anyone knew whether it was possible to tell Gromacs to run for a few hours, dump all the intermediate results and then exit. I was hoping to be able to use the checkpoint function to run the simulation for a bit, checkpoint it, exit then restart. Is this possible? Thanks Natalie Natalie Stephenson, B.Sc PhD Research Associate Manchester Interdisciplinary Biocentre 131 Princess Street Manchester M1 7DN x65816 -- 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] "Command Not Found"
Thanks loads ... that worked perfectly!! Environment configured!! :D
xxx
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Justin A. Lemkul [jalem...@vt.edu]
Sent: 16 May 2011 16:09
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] "Command Not Found"
Natalie Stephenson wrote:
> Sorry for the confusion - didn't mean I'd used a wildcard when typing the
> commands ... just meant I get that response for both commands.
>
> They're an add on created from a the Molecular BioMechanics group
> (http://projects.eml.org/mbm/website/fda_gromacs.htm) - I've downloaded
> they're software as they mention:
>
> Installing the FDAtools package: FDAtools depends on bio3d and SparsM. Please
> download the bio3d package. A a Mac / Linux user, check that your R_LIBS
> variable points to the folder in which packages should be installed (insert
> an export R_LIBS="..." in your .profile / .bashrc if not previously done).
> Install bio3d by executing 'R CMD INSTALL bio3d_1.0-6.tar.gz'. Install
> SparseM by executing 'install.packages("SparseM")' in an R console. Now we
> are ready to install FDAtools, just type 'R CMD INSTALL FDAtools_0.9.tar.gz'
> on the command line.
>
> And downloaded the 'gromacs_4.0.5_pf' that they have (FDA-Gromacs). Is it
> likely to be some problem with the FDA-Gromacs package installation (the one
> I mentioned below) ... or is it likely to be something else?
>
If you're having a problem with some external package, your best bet is to
contact those developers directly. Your previous message said that you were
able to install the package and the executables were in /usr/local/gromacs/bin,
which probably just means your environment isn't configured properly:
http://www.gromacs.org/Downloads/Installation_Instructions#Getting_access_to_GROMACS_after_installation
If the installation was actually successful, this is all you should need to do,
as you would with any Gromacs installation, custom or otherwise.
-Justin
> Thanks Natalie
>
> From: gmx-users-boun...@gromacs.org
> [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul
> [jalem...@vt.edu] Sent: 16 May 2011 15:56 To: Discussion list for GROMACS
> users Subject: Re: [gmx-users] "Command Not Found"
>
> Natalie Stephenson wrote:
>> Hi All,
>>
>> Sorry to bug you all about this - it's been mentioned a few times but I
>> can't find an answer that seems to relate to the situation I've got.
>>
>> I'm trying to use the g_fdaconv / g_fdatools within gromacs 4.0.5, however,
>> everytime I type the commands I get 'g_fda*: command not found'.
>>
>
> Using wildcards will not find command names.
>
>> These are present in the /usr/local/gromacs/bin directory - however when
>> I've checked over the config.log they haven't installed. I'm not sure I
>
> OK, so you have an executable installed, but it didn't install? Can you
> please clarify? Neither g_fdaconv or g_fdatools are standard Gromacs
> utilities - are they some sort of external package or add-on?
>
> -Justin
>
>> understand what's happened - the installation was done by downloading
>> followed by ./configure, make, make install, and everything else seems to
>> be functioning fine. What is it I've missed?
>>
>> Can anyone shed any light on my (probably completely stupid) problem?!
>>
>> Thanks loads, Natalie
>>
>> Natalie Stephenson, B.Sc
>> PhD Research Associate
>>
>> Manchester Interdisciplinary Biocentre 131 Princess Street Manchester M1
>> 7DN x65816
>>
>
> --
>
> Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee
> Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu |
> (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> -- gmx-users mailing list
> gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/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
>
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Departme
RE: [gmx-users] "Command Not Found"
Sorry for the confusion - didn't mean I'd used a wildcard when typing the
commands ... just meant I get that response for both commands.
They're an add on created from a the Molecular BioMechanics group
(http://projects.eml.org/mbm/website/fda_gromacs.htm) - I've downloaded they're
software as they mention:
Installing the FDAtools package:
FDAtools depends on bio3d and SparsM. Please download the bio3d package.
A a Mac / Linux user, check that your R_LIBS variable points to the folder in
which packages should be installed (insert an export R_LIBS="..." in your
.profile / .bashrc if not previously done).
Install bio3d by executing 'R CMD INSTALL bio3d_1.0-6.tar.gz'.
Install SparseM by executing 'install.packages("SparseM")' in an R console.
Now we are ready to install FDAtools, just type 'R CMD INSTALL
FDAtools_0.9.tar.gz' on the command line.
And downloaded the 'gromacs_4.0.5_pf' that they have (FDA-Gromacs). Is it
likely to be some problem with the FDA-Gromacs package installation (the one I
mentioned below) ... or is it likely to be something else?
Thanks
Natalie
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Justin A. Lemkul [jalem...@vt.edu]
Sent: 16 May 2011 15:56
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] "Command Not Found"
Natalie Stephenson wrote:
> Hi All,
>
> Sorry to bug you all about this - it's been mentioned a few times but I
> can't find an answer that seems to relate to the situation I've got.
>
> I'm trying to use the g_fdaconv / g_fdatools within gromacs 4.0.5,
> however, everytime I type the commands I get 'g_fda*: command not found'.
>
Using wildcards will not find command names.
> These are present in the /usr/local/gromacs/bin directory - however when
> I've checked over the config.log they haven't installed. I'm not sure I
OK, so you have an executable installed, but it didn't install? Can you please
clarify? Neither g_fdaconv or g_fdatools are standard Gromacs utilities - are
they some sort of external package or add-on?
-Justin
> understand what's happened - the installation was done by downloading
> followed by ./configure, make, make install, and everything else seems
> to be functioning fine. What is it I've missed?
>
> Can anyone shed any light on my (probably completely stupid) problem?!
>
> Thanks loads,
> Natalie
>
>
> Natalie Stephenson, B.Sc
> PhD Research Associate
>
> Manchester Interdisciplinary Biocentre
> 131 Princess Street
> Manchester
> M1 7DN
> x65816
>
>
--
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] "Command Not Found"
Hi All, Sorry to bug you all about this - it's been mentioned a few times but I can't find an answer that seems to relate to the situation I've got. I'm trying to use the g_fdaconv / g_fdatools within gromacs 4.0.5, however, everytime I type the commands I get 'g_fda*: command not found'. These are present in the /usr/local/gromacs/bin directory - however when I've checked over the config.log they haven't installed. I'm not sure I understand what's happened - the installation was done by downloading followed by ./configure, make, make install, and everything else seems to be functioning fine. What is it I've missed? Can anyone shed any light on my (probably completely stupid) problem?! Thanks loads, Natalie ---- Natalie Stephenson, B.Sc PhD Research Associate Manchester Interdisciplinary Biocentre 131 Princess Street Manchester M1 7DN x65816 -- 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
[gmx-users] Using Gromacs on Condor
Hi, I was wondering if anyone new a way to run mdrun commands through a condor system. I've been told by the people that run our system that unless I can split it into seperate threads then I would not be able to run it as a job, because it would just get stopped in the morning - which from what I've seen would just end my simulation and I would have to start again. Currently my simulations are taking around a month - which as I'm nearing the end of this project is getting quite frustrating as you can imagine. Any ideas on how I can speed this without buying a new computer (which is an idea I've had veeto'd from my supervisor many many times!) would be much appreciated!!! Thanks Natalie -- 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] Problems with pull simulation output - VMD shows broken up groups
Thanks so much ... that's great!! :) Hopefully problem solved! Natalie From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: 03 March 2011 10:50 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Problems with pull simulation output - VMD shows broken up groups Justin A. Lemkul wrote: > > > Natalie Stephenson wrote: >> >> Hi, >> >> I've been having a problem with the pull simulation. After the >> simulation is complete, I use trjconv to separate the pull file into >> seperate .gro's and load this into VMD. When I view it in VMD as the >> 'video' continues parts of amino acids within the protein structure >> seem to jump a long way from the rest of that amino acid leaving a >> long bond between the two, which seems to remain there for the rest of >> the 'video'. Can anyone tell me why this might be happening? And if >> there is a way of solving this problem? >> >> I tried to have a look through the archive for this problem but I have >> no idea what to even search. >> >> I would be immensely grateful for any light you could shed on this >> problem. >> > Sounds like FAQ #11. http://www.gromacs.org/Documentation/FAQs -Justin >> Thanks in advance. >> Natalie >> >> > -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 -- 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
[gmx-users] Problems with pull simulation output - VMD shows broken up groups
Hi, I've been having a problem with the pull simulation. After the simulation is complete, I use trjconv to separate the pull file into seperate .gro's and load this into VMD. When I view it in VMD as the 'video' continues parts of amino acids within the protein structure seem to jump a long way from the rest of that amino acid leaving a long bond between the two, which seems to remain there for the rest of the 'video'. Can anyone tell me why this might be happening? And if there is a way of solving this problem? I tried to have a look through the archive for this problem but I have no idea what to even search. I would be immensely grateful for any light you could shed on this problem. Thanks in advance. Natalie -- 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] Invalid atom number 101717 in indexfile
Thanks for spotting that! I'd thought the system was complete when I'd done the index file - had completely forgot that I'd then gone onto generating ions! Natalie xxx From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: 10 December 2010 13:52 To: Gromacs Users' List Subject: Re: [gmx-users] Invalid atom number 101717 in indexfile Natalie Stephenson wrote: > Hi, > > There are 101987 atoms in my system (2206 from my protein and the rest from > solvent and ions). The index file was made with make_ndx > after creating the solvated box > Command used was "make_ndx -f solv.gro" (solv.gro being the output from > genbox) > But then you added ions? You should make your .ndx file only after the system is complete, otherwise, if you've replaced a water molecule with an ion, the atom index for that atom will belong to a different group. -Justin > Natalie > xxx > > > From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf > of Justin A. Lemkul [jalem...@vt.edu] > Sent: 10 December 2010 12:26 > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] Invalid atom number 101717 in indexfile > > Natalie Stephenson wrote: >> Hi, >> >> I've come across this error when performing grompp of my pull files >> before an afm simulation. I'm not really sure I understand why it's >> saying it ... I've checked over my index file and the atom is part of >> the solvent I've solvated the box with during genbox commands. >> >> The input on the grompp I performed was ... >> grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.trr -o >> pull.tpr >> which produced the error below ... >> >> --- >> Program grompp, VERSION 4.5.3 >> Source code file: readir.c, line: 1371 >> >> Fatal error: >> Invalid atom number 101717 in indexfile >> --- >> What is it I'm doing wrong?! :-S I'm not even really sure where the >> error lies with this one? Is it a step I've performed earlier that's >> incorrect? Can I just remove this atom from the index file and hope for >> the best? >> > > Never make ad hoc changes to any file that Gromacs produces unless you know > the > consequences of doing so. If make_ndx wrote that atom number, it did so for a > reason. > > How many atoms are in your system? How did you create the .ndx file? > > -Justin > >> Thanks loads >> Natalie >> >> >> mdp file I used is below ... >> >> title= Umbrella pulling simulation >> define= -DPOSRES_B >> ; Run parameters >> integrator= md >> dt= 0.001 >> tinit= 0 >> nsteps= 500; 10 ns >> nstcomm= 1 >> ; Output parameters >> nstxout= 5; every 100 ps >> nstvout= 5 >> nstfout= 5000 >> nstxtcout= 5000; every 10 ps >> nstenergy= 5000 >> ; Bond parameters >> constraint_algorithm = lincs >> constraints= all-bonds >> continuation = yes; continuing from NPT >> ; Single-range cutoff scheme >> nstlist= 5 >> ns_type= grid >> rlist= 1.4 >> rcoulomb= 1.4 >> rvdw= 1.4 >> ; PME electrostatics parameters >> coulombtype= PME >> fourierspacing = 0.12 >> fourier_nx= 0 >> fourier_ny = 0 >> fourier_nz= 0 >> pme_order= 4 >> ewald_rtol= 1e-5 >> optimize_fft= yes >> ; Berendsen temperature coupling is on in two groups >> Tcoupl = Nose-Hoover >> nsttcouple= -1 >> tc_grps= Protein Non-Protein >> tau_t= 0.1 0.1 >> ref_t= 310 310 >> ; Pressure coupling is on >> Pcoupl= Parrinello-Rahman >> pcoupltype= isotropic >> tau_p= 1.0 >> compressibility= 4.5e-5 >> ref_p= 1.0 >> ; Generate velocities is off >> gen_vel= no >> gen_temp= 310 >> gen_seed= 1 >> ; Periodic boundary conditions are on in all directions >> pbc= xyz >> ; Long-range dispersion correction >> DispCorr= EnerPres >> ; Pull code >> pull= umbrella >> pull_geometry= distance; can't get PMF with direction >> pull_dim= N N Y >> pull_start= y
RE: [gmx-users] Invalid atom number 101717 in indexfile
Hi, There are 101987 atoms in my system (2206 from my protein and the rest from solvent and ions). The index file was made with make_ndx after creating the solvated box Command used was "make_ndx -f solv.gro" (solv.gro being the output from genbox) Natalie xxx From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: 10 December 2010 12:26 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Invalid atom number 101717 in indexfile Natalie Stephenson wrote: > Hi, > > I've come across this error when performing grompp of my pull files > before an afm simulation. I'm not really sure I understand why it's > saying it ... I've checked over my index file and the atom is part of > the solvent I've solvated the box with during genbox commands. > > The input on the grompp I performed was ... > grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.trr -o > pull.tpr > which produced the error below ... > > --- > Program grompp, VERSION 4.5.3 > Source code file: readir.c, line: 1371 > > Fatal error: > Invalid atom number 101717 in indexfile > --- > What is it I'm doing wrong?! :-S I'm not even really sure where the > error lies with this one? Is it a step I've performed earlier that's > incorrect? Can I just remove this atom from the index file and hope for > the best? > Never make ad hoc changes to any file that Gromacs produces unless you know the consequences of doing so. If make_ndx wrote that atom number, it did so for a reason. How many atoms are in your system? How did you create the .ndx file? -Justin > Thanks loads > Natalie > > > mdp file I used is below ... > > title= Umbrella pulling simulation > define= -DPOSRES_B > ; Run parameters > integrator= md > dt= 0.001 > tinit= 0 > nsteps= 500; 10 ns > nstcomm= 1 > ; Output parameters > nstxout= 5; every 100 ps > nstvout= 5 > nstfout= 5000 > nstxtcout= 5000; every 10 ps > nstenergy= 5000 > ; Bond parameters > constraint_algorithm = lincs > constraints= all-bonds > continuation = yes; continuing from NPT > ; Single-range cutoff scheme > nstlist= 5 > ns_type= grid > rlist= 1.4 > rcoulomb= 1.4 > rvdw= 1.4 > ; PME electrostatics parameters > coulombtype= PME > fourierspacing = 0.12 > fourier_nx= 0 > fourier_ny = 0 > fourier_nz= 0 > pme_order= 4 > ewald_rtol= 1e-5 > optimize_fft= yes > ; Berendsen temperature coupling is on in two groups > Tcoupl = Nose-Hoover > nsttcouple= -1 > tc_grps= Protein Non-Protein > tau_t= 0.1 0.1 > ref_t= 310 310 > ; Pressure coupling is on > Pcoupl= Parrinello-Rahman > pcoupltype= isotropic > tau_p= 1.0 > compressibility= 4.5e-5 > ref_p= 1.0 > ; Generate velocities is off > gen_vel= no > gen_temp= 310 > gen_seed= 1 > ; Periodic boundary conditions are on in all directions > pbc= xyz > ; Long-range dispersion correction > DispCorr= EnerPres > ; Pull code > pull= umbrella > pull_geometry= distance; can't get PMF with direction > pull_dim= N N Y > pull_start= yes > pull_ngroups= 1 > pull_group0= C-Terminal > pull_group1= N-Terminal > pull_init1= 0 > pull_rate1= 0.005 > pull_k1= 1500; kJ mol^-1 nm^-2 > pull_nstxout= 1000; every 2 ps > pull_nstfout= 1000; every 2 ps > -- 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 -- 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
[gmx-users] Invalid atom number 101717 in indexfile
Hi, I've come across this error when performing grompp of my pull files before an afm simulation. I'm not really sure I understand why it's saying it ... I've checked over my index file and the atom is part of the solvent I've solvated the box with during genbox commands. The input on the grompp I performed was ... grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.trr -o pull.tpr which produced the error below ... --- Program grompp, VERSION 4.5.3 Source code file: readir.c, line: 1371 Fatal error: Invalid atom number 101717 in indexfile --- What is it I'm doing wrong?! :-S I'm not even really sure where the error lies with this one? Is it a step I've performed earlier that's incorrect? Can I just remove this atom from the index file and hope for the best? Thanks loads Natalie mdp file I used is below ... title= Umbrella pulling simulation define= -DPOSRES_B ; Run parameters integrator= md dt= 0.001 tinit= 0 nsteps= 500; 10 ns nstcomm= 1 ; Output parameters nstxout= 5; every 100 ps nstvout= 5 nstfout= 5000 nstxtcout= 5000; every 10 ps nstenergy= 5000 ; Bond parameters constraint_algorithm = lincs constraints= all-bonds continuation = yes; continuing from NPT ; Single-range cutoff scheme nstlist= 5 ns_type= grid rlist= 1.4 rcoulomb= 1.4 rvdw= 1.4 ; PME electrostatics parameters coulombtype= PME fourierspacing = 0.12 fourier_nx= 0 fourier_ny = 0 fourier_nz= 0 pme_order= 4 ewald_rtol= 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = Nose-Hoover nsttcouple= -1 tc_grps= Protein Non-Protein tau_t= 0.1 0.1 ref_t= 310 310 ; Pressure coupling is on Pcoupl= Parrinello-Rahman pcoupltype= isotropic tau_p= 1.0 compressibility= 4.5e-5 ref_p= 1.0 ; Generate velocities is off gen_vel= no gen_temp= 310 gen_seed= 1 ; Periodic boundary conditions are on in all directions pbc= xyz ; Long-range dispersion correction DispCorr= EnerPres ; Pull code pull= umbrella pull_geometry= distance; can't get PMF with direction pull_dim= N N Y pull_start= yes pull_ngroups= 1 pull_group0= C-Terminal pull_group1= N-Terminal pull_init1= 0 pull_rate1= 0.005 pull_k1= 1500; kJ mol^-1 nm^-2 pull_nstxout= 1000; every 2 ps pull_nstfout= 1000; every 2 ps -- 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] Pull simulation odditites when viewed in VMD
Thanks loads for that!! I hadn't realised it was that simple! Natalie xxx From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: 09 December 2010 12:05 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Pull simulation odditites when viewed in VMD Natalie Stephenson wrote: > Hey, > > I've been performing a pull simulation of a protein, all seems to work > fine however after I convert the .xtc file into seperate .gro files and > load those into VMD to visualise the simulation something weird > happens. Every 50 frames or so a random bond within the backbone of the > protein (not necessarily near the point of pulling or unfolding) seems > to extend and spike out massively from the structure - does anyone know > why that would be happening? > Please see FAQ #9: http://www.gromacs.org/Documentation/FAQs -Justin > Thanks for your help > Natalie > > -- 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 -- 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
[gmx-users] Pull simulation odditites when viewed in VMD
Hey, I've been performing a pull simulation of a protein, all seems to work fine however after I convert the .xtc file into seperate .gro files and load those into VMD to visualise the simulation something weird happens. Every 50 frames or so a random bond within the backbone of the protein (not necessarily near the point of pulling or unfolding) seems to extend and spike out massively from the structure - does anyone know why that would be happening? Thanks for your help Natalie -- 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
[gmx-users] Pulling Simulation Query
Hi ... Just wondering if there's a way, during pulling simulations, to immobilise say the C-terminus of the protein. I've been running through the 'Umbrella Sampling' tutorial with my own protein. Within this tutorial the ChainB is used as the immobile reference - so it is this that is position restrained. Is there a way of position restraining just one amino acid? How would I specify that in the topology file? Thanks Natalie -- 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] Energy minimisation problems - coordinate file and topology file not matching.
Yeah ... hadn't realised they were there when I began the simulating Natalie xxx From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: 22 September 2010 13:37 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energy minimisation problems - coordinate file and topology file not matching. Natalie Stephenson wrote: > Ok ... think I've worked out what's happened ... > There were two 'SOL' groups. So when replacing solvent with ions it has > added double the amount of ions to the topol.top file. Think I'll go > back a couple of steps and try to sort out why there are two 'SOL' groups. Were there water molecules (i.e., from a crystal structure) in the initial structure passed to pdb2gmx? -Justin > Thanks for the help! > xxx > > > > *From:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on > behalf of Natalie Stephenson [natalie.stephen...@postgrad.manchester.ac.uk] > *Sent:* 22 September 2010 13:02 > *To:* Discussion list for GROMACS users > *Subject:* RE: [gmx-users] Energy minimisation problems - coordinate > file and topology file not matching. > > Thanks for your help Justin & Terry > > I've been letting genion etc update it ... so there must be somewhere > where i've missed it or something. I'll check through the files and see > if I can see what's missing... > > xxx > > > *From:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on > behalf of Terry [terrence...@gmail.com] > *Sent:* 22 September 2010 11:55 > *To:* Discussion list for GROMACS users > *Subject:* Re: [gmx-users] Energy minimisation problems - coordinate > file and topology file not matching. > > > Hi, Natalie, > > Obviously, number of coordinates still doesn't match the topology file > even you updated the topol.top *carefully*. > Check the topol.top thoroughly or paste several line of your coordinate > and topology files may be good ideas. > > Note that the topology file is lacking information for *28* atoms. Does > that number remind you anything? > > > Terry > > On Wed, Sep 22, 2010 at 6:42 PM, Natalie Stephenson > <mailto:natalie.stephen...@postgrad.manchester.ac.uk>> wrote: > > Hi everyone, > > I was hoping you could clear up a problem I'm having when performing > energy minimisation. I'm following the instructions from one of the > tutorials (Justin's Umbrella Sampling) with my own protein, however, > this time when I try to perform the energy minimisation it throws > out this 'fatal error message' ... > > number of coordinates in coordinate file (nrr_solv_ions.gro, 33181) > does not match topology (topol.top, 33153) > > I've been updating the topol.top file every time I've done > something, so I'm not really sure what's happened. > > Can anyone throw some light on what I've gone wrong!! > Thanks loads! > Natalie > > -- > gmx-users mailing listgmx-users@gromacs.org > <mailto:gmx-users@gromacs.org> > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org > <mailto:gmx-users-requ...@gromacs.org>. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- 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 -- 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] Energy minimisation problems - coordinate file and topology file not matching.
Ok ... think I've worked out what's happened ... There were two 'SOL' groups. So when replacing solvent with ions it has added double the amount of ions to the topol.top file. Think I'll go back a couple of steps and try to sort out why there are two 'SOL' groups. Thanks for the help! xxx From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Natalie Stephenson [natalie.stephen...@postgrad.manchester.ac.uk] Sent: 22 September 2010 13:02 To: Discussion list for GROMACS users Subject: RE: [gmx-users] Energy minimisation problems - coordinate file and topology file not matching. Thanks for your help Justin & Terry I've been letting genion etc update it ... so there must be somewhere where i've missed it or something. I'll check through the files and see if I can see what's missing... xxx From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Terry [terrence...@gmail.com] Sent: 22 September 2010 11:55 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energy minimisation problems - coordinate file and topology file not matching. Hi, Natalie, Obviously, number of coordinates still doesn't match the topology file even you updated the topol.top *carefully*. Check the topol.top thoroughly or paste several line of your coordinate and topology files may be good ideas. Note that the topology file is lacking information for *28* atoms. Does that number remind you anything? Terry On Wed, Sep 22, 2010 at 6:42 PM, Natalie Stephenson mailto:natalie.stephen...@postgrad.manchester.ac.uk>> wrote: Hi everyone, I was hoping you could clear up a problem I'm having when performing energy minimisation. I'm following the instructions from one of the tutorials (Justin's Umbrella Sampling) with my own protein, however, this time when I try to perform the energy minimisation it throws out this 'fatal error message' ... number of coordinates in coordinate file (nrr_solv_ions.gro, 33181) does not match topology (topol.top, 33153) I've been updating the topol.top file every time I've done something, so I'm not really sure what's happened. Can anyone throw some light on what I've gone wrong!! Thanks loads! Natalie -- gmx-users mailing listgmx-users@gromacs.org<mailto:gmx-users@gromacs.org> http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org<mailto:gmx-users-requ...@gromacs.org>. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] Energy minimisation problems - coordinate file and topology file not matching.
Thanks for your help Justin & Terry I've been letting genion etc update it ... so there must be somewhere where i've missed it or something. I'll check through the files and see if I can see what's missing... xxx From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Terry [terrence...@gmail.com] Sent: 22 September 2010 11:55 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energy minimisation problems - coordinate file and topology file not matching. Hi, Natalie, Obviously, number of coordinates still doesn't match the topology file even you updated the topol.top *carefully*. Check the topol.top thoroughly or paste several line of your coordinate and topology files may be good ideas. Note that the topology file is lacking information for *28* atoms. Does that number remind you anything? Terry On Wed, Sep 22, 2010 at 6:42 PM, Natalie Stephenson mailto:natalie.stephen...@postgrad.manchester.ac.uk>> wrote: Hi everyone, I was hoping you could clear up a problem I'm having when performing energy minimisation. I'm following the instructions from one of the tutorials (Justin's Umbrella Sampling) with my own protein, however, this time when I try to perform the energy minimisation it throws out this 'fatal error message' ... number of coordinates in coordinate file (nrr_solv_ions.gro, 33181) does not match topology (topol.top, 33153) I've been updating the topol.top file every time I've done something, so I'm not really sure what's happened. Can anyone throw some light on what I've gone wrong!! Thanks loads! Natalie -- gmx-users mailing listgmx-users@gromacs.org<mailto:gmx-users@gromacs.org> http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org<mailto:gmx-users-requ...@gromacs.org>. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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
[gmx-users] Energy minimisation problems - coordinate file and topology file not matching.
Hi everyone, I was hoping you could clear up a problem I'm having when performing energy minimisation. I'm following the instructions from one of the tutorials (Justin's Umbrella Sampling) with my own protein, however, this time when I try to perform the energy minimisation it throws out this 'fatal error message' ... number of coordinates in coordinate file (nrr_solv_ions.gro, 33181) does not match topology (topol.top, 33153) I've been updating the topol.top file every time I've done something, so I'm not really sure what's happened. Can anyone throw some light on what I've gone wrong!! Thanks loads! Natalie -- 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] AFM Pulling Simulations
Quoting "Justin A. Lemkul" : Natalie Stephenson wrote: Hi, I'm a complete novice when it comes to using any kind of command prompt based programmes and hadn't even heard of Linux until my supervisor wanted me to use gromacs ... so needless to say I'm running into a few problems!! I've managed to perform all the generic energy minimisations etc on my protein (basically I can do everything that has been spoon fed to me on the tutorial), but now I want to begin simulating AFM pulling experiments. I've printed (and bound!) the entire manual but I'm still coming up against problems with understanding how I go about running the AFM simulations. Does anyone have a basic syntax they have used to perform a similar simulation so I can work from there and figure out what I need to put where? Also, do I need to create any specific input files for these simulations? Thanks so much for your help with this... A rather inept gromacs user (Natalie!) xxx There is a steered MD component to the umbrella sampling tutorial: http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling Though it is an excellent reference, the manual will not teach you everything you need to know. The mailing list archive (although currently glitching) and Google are your friends, as well. There are hundreds of threads in the archive about pull code success and failure, at least some of which should be informative :) Thanks loads!! I'll give it a try! Natalie xxx -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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] AFM Pulling Simulations
Hi, I'm a complete novice when it comes to using any kind of command prompt based programmes and hadn't even heard of Linux until my supervisor wanted me to use gromacs ... so needless to say I'm running into a few problems!! I've managed to perform all the generic energy minimisations etc on my protein (basically I can do everything that has been spoon fed to me on the tutorial), but now I want to begin simulating AFM pulling experiments. I've printed (and bound!) the entire manual but I'm still coming up against problems with understanding how I go about running the AFM simulations. Does anyone have a basic syntax they have used to perform a similar simulation so I can work from there and figure out what I need to put where? Also, do I need to create any specific input files for these simulations? Thanks so much for your help with this... A rather inept gromacs user (Natalie!) xxx -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
