[gmx-users] g_hbond segmentation fault

Hi Gmxers, I used the command line,  g_hbond -f tst.trr -s tst.tpr -ac test -e 500 -dt 1 and I got the message like, -- Found 1048 different hydrogen bonds in trajectory Found 2292 different atom-pairs within hydrogen bonding distance Merging hbonds with Acceptor

Re: [gmx-users] g_hbond segmentation fault

Hi, Could you file a bugzilla and attach the trr and tpr files please? If you do I'll try to sort it out today or at least this week. Erik Yao Yao skrev 2010-09-29 08.22: I tried without -dt or -e, still the same problem exists in either case. Thanks, Yao --- On *Wed, 9/29/10, David

[gmx-users] 1,4 interactions

Hi all Can someone please get back to me on this. I have generated my own topology file from OPLS parameters by hand with the following format. I am now concerned that I haven't been calculating 1,4 interactions, which I thought were generated by setting gen-pairs = yes. I have read section 5 of

Re: [gmx-users] 1,4 interactions

Gavin Melaugh wrote: Hi all Can someone please get back to me on this. I have generated my own topology file from OPLS parameters by hand with the following format. I am now concerned that I haven't been calculating 1,4 interactions, which I thought were generated by setting gen-pairs = yes.

[gmx-users] g_correlation for version 4.0.7

Dear All, I have been using GROMACS 4.0.7 using the tutorial uploaded by you. I am now trying to analyze my data and have a small request. All the modules related to g_correlation is available only for version 3.3.3.1 which are not accepting the xtc files from version 4.0.7. Are there any

[gmx-users] lipids number

Hi, I am not sure someone asked some similar questions before or not. From Prof. Peter Tieleman's website we can get the 128 lipids pdb file. Are there some trick and easy way to multiply those lipids . I mean, Suppose I need 640 dppc lipids, how can I get those coordinates easily from those

Re: [gmx-users] topolbuild cannot open logfile

Thanks very much for your reply yes i was just being daft and trying to run things from the wrong place therefore wrong permissions! Also i was pointing to the wrong directory for force fields. Things are working now. Thank you once again Andrew --- On Wed, 29/9/10, Bruce D. Ray

Re: [gmx-users] lipids number

#ZHAO LINA# wrote: Hi, I am not sure someone asked some similar questions before or not. From Prof. Peter Tieleman's website we can get the 128 lipids pdb file. Are there some trick and easy way to multiply those lipids . I mean, Suppose I need 640 dppc lipids, how can I get those

RE: [gmx-users] lipids number

I have a vague impression about that, seems someone asked similar things before. I will do a try and see. Thanks, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Wednesday,

Re: [gmx-users] 1,4 interactions

Gavin Melaugh wrote: Hi Justin Thanks for replying. I have checked the energy file and there are no 1,4 terms, which is what I expected. I should clarify that my parameters are taken from the OPLS ua forcefield but I have relabelled them for my own model, which is not a common molecule.

Re: [gmx-users] 1,4 interactions

A few points then, 1) So a [pairs] directive would include all the atom indices of the 1,4 interactions and the coressponding values of sigma and epsilon?, which I would do manually. 2) In the manual it says ''gen-pairs = yes : generate 1,4 interactions which are not present in the pair list

Re: [gmx-users] 1,4 interactions

Gavin Melaugh wrote: A few points then, 1) So a [pairs] directive would include all the atom indices of the 1,4 interactions and the coressponding values of sigma and epsilon?, which I would do manually. No. A [pairs] directive simply lists the pairs of atoms for which 1,4 interactions

Re: [gmx-users] 1,4 interactions

Right, I think the penny has finally dropped. On the back of what you said. 1)In my topologies I have always listed say a [bond] directive, with bond indices,function, k, and r0. I could however just list the indices and the function, and then have the corresponding parameters in the [bond types]

Re: [gmx-users] 1,4 interactions

Gavin Melaugh wrote: Right, I think the penny has finally dropped. On the back of what you said. 1)In my topologies I have always listed say a [bond] directive, with bond indices,function, k, and r0. I could however just list the indices and the function, and then have the corresponding

Re: [gmx-users] 1,4 interactions

Hi Justin I just wanted to say a big thanks for your time and patience Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Right, I think the penny has finally dropped. On the back of what you said. 1)In my topologies I have always listed say a [bond] directive, with bond

Re: [gmx-users] 1,4 interactions

Gavin Melaugh wrote: Hi Justin I just wanted to say a big thanks for your time and patience No problem. This exchange has made me realize that what's in the manual, while complete, lacks a bit of clarity. I'm going to make some updates to the documentation for a future release.

[gmx-users] g_clustsize not recognize the -mol option and ignore the index file

Hello everybody, I'm using g_clustsize to analyze clusters formed in my solution. However I noticed that not would get consistent results using the complete trajectory (containing both solvent and solute). To see the aggregation, using g_clustsize, I had to convert my trajectory to a file

[gmx-users] rlist and rlistlong in gmx451

Dear Gromacs Users and Developers, I am testing gromacs-4.5.1 with different running parameters, in particular switching potentials and rlistlong. I have a question about this NOTEs given by grompp when rlist=rvdw=rcoulomb (I thought that was rlonglist that should be longer than rvdw and

Re: [gmx-users] 1,4 interactions

Justin One last question.What is the point of the [nonbond_params] directive if all your LJ parameters are already specified in [atomtypes]?, also [pairs_nb]. Surely it is not necessary to list all nb pairs? Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin I just wanted to say

Re: [gmx-users] rlist and rlistlong in gmx451

Carlo Camilloni wrote: Dear Gromacs Users and Developers, I am testing gromacs-4.5.1 with different running parameters, in particular switching potentials and rlistlong. I have a question about this NOTEs given by grompp when rlist=rvdw=rcoulomb (I thought that was rlonglist that should be

Re: [gmx-users] 1,4 interactions

Gavin Melaugh wrote: Justin One last question.What is the point of the [nonbond_params] directive if all your LJ parameters are already specified in [atomtypes]?, also You can define non-standard parameters here. Otherwise, the normal combination rules are used. It seems like, at least

[gmx-users] Pull Code for Secondary Stability

Does anyone know if the pull code can be used to determine structure stability? If I wanted to generate a stress-strain plot of an alpha-helix, would the pull simulation give me the data such as the force vs displacement? Thanks -- gmx-users mailing

[gmx-users] viscosity calculation

Hello, I used g_energy –f *.edr –vis *.xvg –s *.tpr to calculate the viscosity of my system which is water. Two files are generate: *.xvg and the enecorr.xvg. Now, what should I do to calculate the viscosity of my system with these two files? Sorry for such naïve question. Regards, Payman

Re: [gmx-users] viscosity calculation

Payman Pirzadeh wrote: Hello, I used g_energy –f *.edr –vis *.xvg –s *.tpr to calculate the viscosity of my system which is water. Two files are generate: *.xvg and the enecorr.xvg. Now, what should I do to calculate the viscosity of my system with these two files? Sorry for such naïve

RE: [gmx-users] viscosity calculation

Well, two questions: 1. My bulk values are fluctuating around 60 (I assume cP). But it looks like very weird to me since experimental value for water viscosity is 0.854 cP. My system is at 265K with 4202 molecules. Is sth strange going on? Or I am missing some unit conversions in the plot. 2.

[gmx-users] Steered molecular dynamics and Parinello-Rahman and bond constraints.

Hi GMX-users, I am beginning to use the steered molecular dynamics method to perform a potential of mean field calculation. In your experience, does it matter what kind of a thermostat and pressure coupling is used? Does Nose-Hoover and Parinello-Rahman perform better than Berendsen for this

Re: [gmx-users] viscosity calculation

On 2010-09-29 20.52, Payman Pirzadeh wrote: Well, two questions: 1. My bulk values are fluctuating around 60 (I assume cP). But it looks like very weird to me since experimental value for water viscosity is 0.854 cP. My system is at 265K with 4202 molecules. Is sth strange going on? Or I am

Re: [gmx-users] Steered molecular dynamics and Parinello-Rahman and bond constraints.

quantrum75 wrote: Hi GMX-users, I am beginning to use the steered molecular dynamics method to perform a potential of mean field calculation. In your experience, does it matter what kind of a thermostat and pressure coupling is used? Does Nose-Hoover and Parinello-Rahman perform better than

Re: [gmx-users] viscosity calculation

265 K is -8C, so ice, not liquid water. That would be more viscous than you might expect. Waren Gallin On 2010-09-29, at 12:52 PM, Payman Pirzadeh wrote: Well, two questions: 1. My bulk values are fluctuating around 60 (I assume cP). But it looks like very weird to me since experimental

RE: [gmx-users] viscosity calculation

Apparently, in the file the unit in the file is cP. It might be the case that I plotted the wrong column. I think I should get the third column. Regarding the diffusion, I read in papers about rotational diffusion of the proteins which could be calculated having the viscosity of the liquid and

[gmx-users] Re: Problem with pressure coupling

Hi again, I have made available a testcase that reproduces the problem here: http://marge.uochb.cas.cz/~marsalek/tmp/test-volume-drift.tar.bz2 To see the problem, use grompp from GMX 4.5.1 and run the resulting tpr. Then extract the volume: echo Volume | g_energy -f ener.edr -o volume and

Re: [gmx-users] Re: Problem with pressure coupling

On 2010-09-29 21.15, Ondrej Marsalek wrote: Hi again, I have made available a testcase that reproduces the problem here: http://marge.uochb.cas.cz/~marsalek/tmp/test-volume-drift.tar.bz2 To see the problem, use grompp from GMX 4.5.1 and run the resulting tpr. Then extract the volume: echo

RE: [gmx-users] viscosity calculation_2

Adding to my previous comments, It looks like that the third column is the appropriate one to plot. However, I tried to use g_energy -b 0 -e 2 to take the whole trajectory (2 ps) rather than half of the frames. But, still g_energy take half of the frames. This has caused improper

Re: [gmx-users] viscosity calculation_2

On 2010-09-29 22.00, Payman Pirzadeh wrote: Adding to my previous comments, It looks like that the third column is the appropriate one to plot. However, I tried to use g_energy -b 0 -e 2 to take the whole trajectory (2 ps) rather than half of the frames. But, still g_energy take half of

Re: [gmx-users] Re: Problem with pressure coupling

On Wed, Sep 29, 2010 at 21:56, David van der Spoel sp...@xray.bmc.uu.se wrote: Now the differences in the tpr files are revealing: [anfinsen:test-volume-drift] % gmxcheck -s1 topol405.tpr -s2 topol.tpr snip Note: tpx file_version 58, software version 73 Reading file topol.tpr, VERSION

RE: [gmx-users] viscosity calculation_2

Thanks for the tips. I just realized that there two other outputs two the g_energy -vis: evisco.xvg and eviscoi.xvg These files contain 5 columns among which the first one looks to be time. But what are the other 4? What are their differences? Regards, Paymon -Original Message- From:

[gmx-users] distance restrained D simulations

Hi! I am trying to perform distance restrained MD simulations of a protein with Gromacs4.0.5. I have a bunch of FRET distances ranging from 10Angs to 40 angs that I am incorporating simular to NOE distance restraints in NMR. When I use one processor for the simulations its all fine, but, when I

Re: [gmx-users] distance restrained D simulations

jayant james wrote: Hi! I am trying to perform distance restrained MD simulations of a protein with Gromacs4.0.5. I have a bunch of FRET distances ranging from 10Angs to 40 angs that I am incorporating simular to NOE distance restraints in NMR. When I use one processor for the simulations

Re: [gmx-users] distance restrained D simulations

What is happening is that you've got bonds too long and the dd can not manage to cut things in 4 subsystems ... try particle decomposition but you might end up with the same problem :(( On Sep 29, 2010, at 5:35 PM, jayant james wrote: Hi! I am trying to perform distance restrained MD

Re: [gmx-users] distance restrained D simulations

Yes you are right particle decomposition does not work too! On Thu, Sep 30, 2010 at 12:19 AM, XAvier Periole x.peri...@rug.nl wrote: What is happening is that you've got bonds too long and the dd can not manage to cut things in 4 subsystems ... try particle decomposition but you might end

RE: [gmx-users] viscosity calculation_2

Sorry, haven't looked at these files before so this might not be the case, but doesn't the top of the .xvg file explain what each column is? Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville