[gmx-users] COM Pulling - Single Chain

Warren, You're right that one can not use constraints if they are also using lincs on C-C bonds. However, constraining this bond is not necessary with a 1 fs timestep. Even while constraining C-C bond lengths, one can still use harmonic restraints instead (also from the pull code). Before

[gmx-users] Simulation parameter problem about protein unfolding

Thanks David. I think that we're saying the same thing, but there is indeed a 'correct' denatured state at a given temperature and pressure and protein concentration and salt concentration, etc. It was this to which I was referring. Chris. On 2010-10-18 06.56, chris.neale at utoronto.ca

[gmx-users] Simulation parameter problem about protein unfolding

Chen, to answer this, please see David's post and my reply. To answer if your unfolded state ensemble is accurate, you will need to know some experimentally evaluated quantities of the state that you are trying to reproduce: 498K, 26 atm, a certain amount of salt, etc, (but not including

[gmx-users] Simulation parameter problem about protein unfolding

Generally, forcefields are not parameterized for temperatures other than 298K, so simulations are not expected to reproduce the expected properties (like boiling water and the correct temperature denaturation of proteins). There's almost certainly other issues here (including the fact that

[gmx-users] Questions about REMD calculations

Stefane, for more information on what Mark is talking about here, check out his publication: M. J. Abraham and J. E. Gready (2008) Ensuring Mixing Efficiency of Replica-Exchange Molecular Dynamics Simulations J. Chem. Theory Comput. (4), 1119-1128. Dear all, I come back to you for several

[gmx-users] g_hbond results inconsistent between v4.0.7 and v4.5.1

Has anybody checked g_hbond results for consistency between v4.0.7 and v4.5.1? My usage is: g_hbond -f my.xtc -r 0.68 -contact -life -s my.tpr -ac and I find that the output files hbnum.xvg, hbac.xvg, hblife.xvg, and the ac-reported lifetime of interactions are all different. To show the

[gmx-users] g_hbond results inconsistent between v4.0.7 and v4.5.1

If I redo this, selecting only a single acceptor atom and 64 donor atoms, with a large cutoff distance of 3 nm, v4.0.7 gives me 44 should have read 4 nm above. the point is that there really are 44 contacts, but v4.5.1 reports only 1. contacts in one frame while v4.5.1 gives me only 1

[gmx-users] Questions about REMD calculations

Stefane, why are you hesitant to reduce the size of your system. If you can still address the same questions with a smaller system, then I'd say the answer is nearly always to use that smaller system (REMD or not). Besides, my gut feeling is that even if you had enough 271*16 cpus

[gmx-users] why does trjcat take so much memory?

Thank you David, Berk, and Roland. unix cat is a good option (I didn't realize that this was possible) and so is scripting to do it in a number of steps. I have filed enhancement request #593. Thank you, Chris. --- original message --- On 2010-10-13 01.54, chris.neale at utoronto.ca

[gmx-users] free energy decomposition

Sanku, This is not possible using g_energy or any other gromacs tool that I am aware of. You must calculate the temperature derivative of the free energy. See, for example, equation 16 in Pettitt BM, Rossky PJ. J Chem Phys. 1986;84:5836 -- original message -- Hi, I am studying Potential of

[gmx-users] REMD speed calculation compared to classical MD

Stefane, If you are asking for a comparison of simulation time required, then that is not something that can be answered in the abstract. There are even cases in which REMD will take more total simulation time to converge the 300K ensemble than will N simulations all at 300K. The efficiency

[gmx-users] free energy decomposition

Sanku, decomposing free energies into enthalpic and entropic components is not my particular expertise, but I'm astounded to hear that enthalpy equals the average forcefield energy. I would have thought that, at the very least, pressure work would also need to be incorporated. Honestly, I

[gmx-users] why does trjcat take so much memory?

Thank you for the insight Mark. To get it on the record, this is fairly annoying for trjcat (not trjconv). If anyone else has run into this, then please do post because a memory efficient cat mechanism will only be coded if there is sufficient interest. But again, thanks for your good

[gmx-users] about COM pulling and g_dist

Dear Zhongjin: 1. You have indeed provided more data, but please try to make some progress on your own. E.g. you tell me the order of selections into g_dist, but you should try reversing the order. 2. Your figures are difficult to interpret -- I only opened Snap5, but I don't know what

[gmx-users] about COM pulling and g_dist

Dear Zhongjin: First, I see no reason why you would not expect your g_dist values to be negative. If you want the positive distances, then reverse the order of the groups as you pass then to g_dist. Also, what type of values do you get directly out of mdrun and into the pull_x.xvg file?

[gmx-users] How to make a lipid bilayer with specific dimensions?

I don't think that this is currently causing anybody any problems, but note that genbox is going to cut any lipids that cross out of the central unit box (either because genbox is unaware of PBC or because these lipids now clash across PBC). Therefore: genbox -cs popc128a.pdb -o

[gmx-users] PMF on dihedral

Landry, I replied earlier, but it didn't seem to make it to the list. If 2 show up then they are identical. The mailing list archive post that you cite is actually talking about a (3-point) angle and not a (4-point) dihedral angle. If you want dihedral angles, then take a look at how

[gmx-users] PMF on dihedral

Landry, you can't do it using the pull code, but it is possible. We did US over Phi and Psi in the following paper, and you can get the methods from there. I also posted many more specifics and examples to the mailing list during that time. C. Neale, T. Rodinger, and R. Pomès,

[gmx-users] Umbrella sampling question

Aswathy: We can't tell if you did US correctly unless you post what you have done. You must give more info and you must copy and paste the actual input / .mdp parameters that you used. As for if your PMF is correct, then we can never tell you that. You can, however, ensure that your

[gmx-users] PBS script

Manoj, to suggest that Justin is being lazy would be to ignore the hundreds, possibly thousands, of helpful posts that he has made on the gromacs mailing list to assist users like yourself free of charge. In fact, Justin was probably helping you more than you have realized by pointing

[gmx-users] restraining atoms to the plane at the bilayer center: pull code ?

Maria, I highly doubt that you are correct. If you want more help, please copy and paste your commands and some relevant output back to the list. Chris. --original message -- Message: 4 Date: Wed, 8 Sep 2010 15:07:15 +0200 From: maria goranovic mariagorano...@gmail.com Subject: Re:

[gmx-users] restraining atoms to the plane at the bilayer center: pull code ?

Maria, try this. There actually is a lot of this on the mailing list, so I suggest checking it a little deeper for your next querry, or at least outlining how you looked and what you found so that it is clear you have tried. Also, read about pull_pbcatomN and think carefully about how you

[gmx-users] Re: Re[7]: Flat energy profile in g_wham

Sorry Alex, but there is no good substitute what I have already suggested. I helped you find a lead and I suggested a way to simplify your system to discover what is going on. Now it's up to you to do that work. It might end up being a bug, but I doubt it. I have done things similar to

[gmx-users] pbc in one direction only for analysis?

It's a messy solution, but you could 1. run trjconv so that your cylinder is in the unit cell 2. convert your trajectory to .gro files 3. massively expand the x and y dimensions of each .gro 4. join the .gros to a .xtc 5. g_rdf You could also use template.c to write a program that does this

[gmx-users] Re: Re[9]: Flat energy profile in g_wham

Can you post a snip of your pullx and pullf files from the water box simulation where you pulled on 2 waters? Quoting alexander yakovenko yakovenk...@ukr.net: Yep, my case is b  :(... Gromacs do writes pullx as ref COM global coords and pull COM displacement. And I still don't realize what

[gmx-users] Re: Re[11]: Flat energy profile in g_wham

Alex, If you do decide to continue along with the method that I suggested, I'll join back in. To this point, I see no indication that you have tried to relate the force to the position for the water runs, which is my standing suggestion to you. Chris. Quoting alexander yakovenko

[gmx-users] Flat energy profile in g_wham

Alexander: Can you please also post your free energy profile out of wham? Also, can you confirm that you are using different force constants for different windows? Justin is correct, but that just means that you are using more cpus than you need... it's not actually wrong. What are your

[gmx-users] Flat energy profile in g_wham

Alexander, please post the following: 1. force constants for your plot at http://picasaweb.google.ca/117558205101329348732/G_wham#5511287294315721970 NOTE: if they are all 1000 as in your first post, then you have a problem in your sampling. 2. units for your x-axis in the plot mentioned

[gmx-users] Re: Re[5]: Flat energy profile in g_wham

First, I don't think that you converted and debiased correctly. Once you have a histogram of the displacement, then you will debias that histogram like this (assuming run at 298K): FC=1000 T=298 cat biased.hist |awk '{print $1,-0.00831447*'${T}'*log($2)-0.5*'${FC}'*$1*$1}' debiased.hist

[gmx-users] Re: Re[7]: Flat energy profile in g_wham

First, you confuse me when you say pulling direction was along Y-axis since your .mdp file indicates pull_dim = Y Y Y and so you are pulling in *all* dimensions. Your profile doesn't look like mine at all, but then again I took mine from a force profile. Now that I can see your forces and

[gmx-users] Re: Re[7]: Flat energy profile in g_wham

So now we have the first real lead. Next is for you to simplify your system to the point where you *can* understand the relationship between the pullf and pullx files. For example, I always suggest a water bath of explicit water with the sd integrator and apply the pull code to two waters.

[gmx-users] How to control and interpret g_density analysis more precisely?

Dear Alex: be careful with g_density! If you do not use the symmetrize -symm option, then the box height is going to be taken as a single frame. If you do NpT, then you will get an incorrect (or at least noisy) result. I forget if this will bite you if you do use the -symm option. This

[gmx-users] pbc atom

Gavin, I recall mentioning gen_vel=no with temperature coupling as a possible problem a while ago (the problem is that the initial forces become initial velocities and then those get scaled up and what you have are velocities and not temperatures -- read about the flying ice cube problem).

[gmx-users] Molecule out of pbc box

Dear Nimesh: trjconv -f orig.xtc -s my.tpr -o new.xtc -pbc atom to get the help information: trjconv -h Normally, you might not get an answer to this one since it's the most commonly asked question. The users list search is, however, not working right now so I thought I'd pass along the

[gmx-users] gromacs users list search for molecule returns zero results

I think that there is some problem with the users list search on the gromacs page: http://www.gromacs.org/Support/Mailing_Lists/Search A gromacs users list search for molecule returns zero results. A search for gromacs does return lots of results. A google search for gromacs and molecule

[gmx-users] pbc atom

velocities are not taken from the .gro as far as I know. You can get them from the .trr if you also use a .edr. If you want to check, then do a run for only 1 ps and save your .edr every timestep. Then run g_energy and look at the temperature. I am not sure that a constant energy

[gmx-users] AFM Pulling Simulations

Natalie: It would also be a good idea for you to ensure that your supervisor knows how difficult it is to learn and correctly apply these methods. If they think that a person can learn linux and gromacs and the gromacs pull code in a short period of time, then the stage is set for

[gmx-users] pbc atom

I have seen this before, and there are a few possible reasons, but I'm still waiting to see that histogram with two peaks (http://lists.gromacs.org/pipermail/gmx-users/2010-August/053311.html). It's really hard to help you when we have to guess what the problem looks like... or perhaps you

[gmx-users] pbc atom

Yup, just got the link. Thank you for posting, and sorry that I missed it. It seems possible that Justin is correct and you'll get good data if you take it out of the pullx.xvg file (perhaps the g_dist tool is wrapping pbc for you). 1. How big is your box definition in your .gro file? You

[gmx-users] pbc atom

Dear Gavin: What happens if you replace your reference group by a single water molecule and your pulled group by a single water molecule and run the 2.35 nm simulation again. Do you get the same two-peaked histogram? What about if you use a system with a single water for the reference

[gmx-users] pbc atom

Tsjerk, Two reasons. First, I simply don't understand awk as well as you do. Second, I think that breaking it down into simpler commands linked by pipes is better for teaching. If somebody needs help to combine 3 cols into a vector distance, then they may copy and paste your solution to

[gmx-users] umbrella histograms

Gavin, thank you for plotting the sampling by the time. Looks like this isn't a two state problem. Can you also show a histogram image on-list please? Just a histogram of the sampled distances. Thanks, Chris. Sorry forgot to attach the files Hi Chris Sorry for the delay. Please find

[gmx-users] ener.edr

The .edr file contains the instantaneous energies at every nstenergy steps. -- original message -- Hello, Does gromacs write the current values (at some requested step) to ENER.EDR or the averaged ones (at the requested interval)? -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] umbrella histograms

As I said before, please plot the position vs. time. It would be best if you can make a graph of this and post it to some web tool. I use photobucket, but there are many others. I realize that you think you are starting at equilibrium, but there are always things that can have unexpected

[gmx-users] umbrella histograms

Gavin, I wish you the best of luck. Perhaps somebody else on the list can help you. -- original message -- Thanks Chris I have equilibrated the system at 600 K in a previous run therefore would it not be equilibrated, and also would the velocities from the final configuration of the

[gmx-users] umbrella histograms

Your language was not rude, but I did get frustrated after twice asking you to perform an analysis and twice being ignored. My advice still stands: plot the deviation vs. time and report back to the list. Chris. -- original message -- Cheers and thanks for the suggestions. P.S. I hope you

[gmx-users] umbrella histograms

Dear Gavin: plot the position vs. time. Probably you will see it sample around one value, then discover a new state, and make a sharp transition to another value. If the new state is much more favourable than the initial state, then you can discard the initial state as equilibration. It

[gmx-users] Units of k1 in the pulling code

Dear Xueming: the word mol is short form for mole http://en.wikipedia.org/wiki/Mole_%28unit%29 In the pull code context, it refers to moles of the pulled group. The force is not applied to the COM of a cluster. The magnitude of the force is determined based on the COM distance, and then the

[gmx-users] GPU CUDA version does not support improper dihedrals?

This surprised me since most of the systems that I am interested in have improper dihedrals. Is it possible that I did something wrong here? ### Error message from mdrun-gpu: Program mdrun-gpu, VERSION 4.0.99-dev-20100315 Source code file:

[gmx-users] compiling GPU 4.5b2, CUDA_INCLUDE_DIRECTORIES function is undefined

Thank you Rossen, that worked. When I compile, should I be including my FFTW as per normal? I didn't do that since it was not mentioned and during the build, I get -- Using internal FFT library - fftpack --- original message --- Hi Chris, ## what I did: module purge module load

[gmx-users] abnormal stop of job

This sounds like you, or your sysadmin, killed the job. It is also possible if you are using a cluster that there is a walltime limit and you exceeded that, so your job was sent the term signal. You should restart the run. Check the manual on how to do that since it depends on what version

[gmx-users] GPU version does not support improper dihedrals?

This surprised me since most of the systems that I am interested in have improper dihedrals. Is it possible that I did something wrong here? ### Error message from mdrun-gpu: Program mdrun-gpu, VERSION 4.0.99-dev-20100315 Source code file:

[gmx-users] hyperthreading

I haven't tried mdrun -nt based hyperthreading, but I have tested using -np 16 on an 8 core box. I get an 8% to 18% performance increase when using -np 16 and optimizing -npme as compared to -np 8 and optimizing -npme. This is on a cluster of Intel Xeon E5540 aka Nehalem with 2 quad cores

[gmx-users] abnormal stop of job

Sounds like you killed the job, or your sysadmin killed it, or it timed out if you are on a cluster with a walltime limit. -- original message -- Hi all, I have been running a simulation of 200 ns length and it suddenly stoped at 67 ns showing the following line - Received the TERM

[gmx-users] Conformational sampling

Nisha, The approach is dictated by the goal. What do you want from this? and why are you doing it? e.g. if you want to test the FF, then it is a good idea to at least include US as a part of your strategy; if you want to determine if 100 ns of equilibrium sampling is sufficient to

[gmx-users] Conformational sampling

Nisha: Simply applying available tools and seeing if the distribution looks okay is not a good plan. You should have a very well-defined idea of what you are trying to test and then pick a tool to get that done. For example, perhaps you have a reference that provides the converged

[gmx-users] compiling GPU 4.5b2, CUDA_INCLUDE_DIRECTORIES function is undefined

Dear Szilárd and Rossen: I have attempted with gcc4.4.0 and I got the same result. I can verify that cmale/FindCUDA.cmake exists and contains the MARCO for CUDA_INCLUDE_DIRECTORIES but it seems that this library is not, for some reason, getting loaded in by at least

[gmx-users] compiling GPU 4.5b2, CUDA_INCLUDE_DIRECTORIES function is undefined

Dear users: I previously posted about difficulties compiling gromacs 4.5b2 for GPUs: http://lists.gromacs.org/pipermail/gmx-users/2010-August/052905.html It turns out that this problem was not directly related to version. First, I had to add -DLIB_INSTALL_DIR=$(pwd)/install_dir to the cmake

[gmx-users] What version of cmake is required to compile v4.5b2 for GPUs?

Thanks Rossen, I did not yet get it working. I just posted under a more relevant title, please see the post: http://lists.gromacs.org/pipermail/gmx-users/2010-August/052939.html (there were 2 errors, one that I fixed and one that I am still struggling with). Chris. -- original message --

[gmx-users] compiling GPU 4.5b2, CUDA_INCLUDE_DIRECTORIES function is undefined

It turns out that I can make the error message with CUDA_INCLUDE_DIRECTORIES go away by adding the following text to kernel/gmx_gpu_utils/CMakeLists.txt MACRO(CUDA_INCLUDE_DIRECTORIES) FOREACH(dir ${ARGN}) SET(CUDA_NVCC_INCLUDE_ARGS ${CUDA_NVCC_INCLUDE_ARGS} -I${dir}) ENDFOREACH(dir

[gmx-users] v4.5b2 error specifically on 16 cores with npme 6

Dear all: I have an explicit solvent peptide-in-bilayer system taht also used the pull-code. This system runs fine on 8 cores in a single box with v4.0.7 and 4.5b2. It also runs fine on 16 cores IB for v4.0.7 but not 4.5b2. In the later case, I get an exit from mdrun (see below). I have

[gmx-users] What version of cmake is required to compile v4.5b2 for GPUs?

It seems that cmake 2.8.0 is not recent enough? I attempted to compile like this: cd /project/pomes/cneale/GPC/exe/intel/gromacs-4.5-beta2 module purge module load intel module load cuda #cuda 3.0 module load cmake#cmake 2.8.0 export CC=icc export CXX=icpc cmake

[gmx-users] What version of cmake is required to compile v4.5b2 for GPUs?

Ah, I see that I need version =2.6.4 This info is on the web, but not in the INSTALL_GPU file... perhaps that file could include all of the information found here: http://www.gromacs.org/index.php?title=Download_%26_Installation/Related_Software/Gromacs_on_GPUs Thanks, Chris. -- original

[gmx-users] Pullx file

Dear Aswathy: When you post to the list, you should include a description of what you eventually want to do. Here's an example of why this is important. If you want to make PMF then you must use the values of the pulled group. I'm not promoting using SMD to make PMFs, but since it is

[gmx-users] gromacs energies very different from other MD engine for the very same system and conditions

Dear Alan: I don't have a solution for you, but I do have a simpler test case: a single spc water molecule. I have not addressed your noted energy difference between programs because I am not familiar with them (although you should try gromacs compiled in double precision). I can

[gmx-users] pull code example

I'd send a list of links except that the other end of a google search for gromacs pull code example has all of what you will need to broaden your general pull code understanding. The mailing list has an absolutely massive number of posts on this too. Chris. Hi all, Could anybody please

[gmx-users] Re: selenium parameter

Susan. Please use the mailing list instead of personal email. A google search for electronegativity of selenium provides a useful first hit. The .rtp issue is covered often on the mailing list. Overall, you will find this link helpful:

[gmx-users] HA1/HA2 chirality of GLY

Dear Ehud: A quick google search turned up: http://www.bmrb.wisc.edu/ref_info/atom_nom.tbl # A.A. BMRBSC PDB UCSFMSI XPLOR SYBYL* MIDAS* DIANA # - - - - G HA2 pro-R

[gmx-users] high repulsion in packed system

Dear Shuai: When you get some advice, it's useful if you can try it before coming back to the list. Vitaly was simply giving you an idea about how to proceed. You need an initial state that it high-density and this is one way to get such a state fairly easily: start with a low density

[gmx-users] problems with g_wham

Depending on your system and chosen thermostat, gen-vel=no can be a dangerous idea (very small original velocities simply get scaled up); besides, you should be able to equilibrate from a gen-vel=yes pretty quickly. I don't disagree with Justin's comment, but just because it works doesn't

[gmx-users] problem with trjconv -pbc cluster

Dear Jagannath: There is, as far as I know, no way to fix this. Here's what you should do. 1. Let the space between your timesteps be X ps. 2. Use trjconv -pbc cluster -dump X -o out.gro 2b. if that doesn't work, try trjconv -pbc cluster -dump (X*2) -o out.gro 2c. if that doesn't work, try

[gmx-users] problem with trjconv -pbc cluster

PS: you realize that trjconv -pbc cluster is never going to work unless you actually have a cluster, right? So you can't start this procedure near your initial dispersed state. You need to start at some time T where you actually do have a cluster. Then you can try -dump T, -dump (T+X),

[gmx-users] Frozen N2 in a very long tube; was help: gromacs mistake

Dear shuai shuai: Please use a descriptive title. I renamed it. You must describe your problem more. e.g. is the problem that you get a frozen cluster in some simulations, or that you don't get this in other simulations? What, exactly, is a small cluster of frozen molecules? You must

[gmx-users] wrong charge assignment(?) on ATP in rtp file

Dear Shuntaro: If you're using PME then there is no need to have unit charge in charge groups. I can't comment on any other errors that may or may not be in that topology as I have never simulated ATP. Also, if you're not using PME, then I can not advise you if it is ok to have non-integer

[gmx-users] how gromacs calculate center of mass for broken molecules?

That depends. mdrun pull code does it smartly via pull_pbcatom (assuming that you have chosen pull_pbcatom and your box size smartly), while g_dist is not smart about it at all. Can you be more specific about what you want to do? -- original message -- Hi everyone: How gromacs calculate

[gmx-users] problem with trjconv -pbc cluster

I wrote my own program to do this and so I never tried that one. We did find that clustering based on a dingle atom in the chain was a very good idea. So take your distal carbon in the surfactant and make in index group of it and cluster it (with a larger cutoff) with g_clustsize.

[gmx-users] COM distances

The pullx file should contain everything that you need. dX,dY,dZ *are* the components of the distances between the two groups. I still don't understand your question (perhaps you could give us a worked example with real data?), but if you just want the COM distance, then try this: cat

[gmx-users] problem with g_clustsize

perhaps that's not standard terminology, sorry. The numbering starts at the headgroup so the distal atom would be the one at the end of the acyl-chain (the one most likely to spend its time in the middle of the cluster. -- original message -- Thanks. Just wondering what is a 'distal atom'

[gmx-users] problems with g_wham

Gavin, let's take g_wham out of the picture for now to simplify things. First, you umbrella is pretty strange. You want them to have a distance of 0.0 nm (pull_init1 = 0)??? So let's look at making a histogram from your raw data. 1. cat pullx.xvg |awk '{print sqrt($1,$5*$5+$6*$6+$7*$7)}'

[gmx-users] problems with g_wham

Gavin, I think it's time for you to read some papers and read the gromacs manual pull COM section. A few days of reading will make all of this clear to you. -- original message -- Hi Chris Thanks very much for your help. The reason I used pull_init1 = 0 is because this is the value that

[gmx-users] wrong charge assignment(?) on ATP in rtp file

It seems that I do not need to care about decimal total group charges as I am planning to use PME. -- well, find it in the literature first! -- original message -- Dear Chris, I really appreciate your comment. Can you provide a reference for the idea that the charge groups must have

[gmx-users] problems with g_wham

I missed that pull_start = yes, sorry. So Gavin, your run should have stayed around the starting position. Make the histogram directly and you should get a better idea. Chris. -- original message -- To clarify, the tutorial sets pull_init1 = 0 because it is used in conjunction with

[gmx-users] Parameters for selenium

I don't have the parameters. You could possibly fudge it by extrapolating out from SER-CYS-Se_CYS based scaled by electronegativities of O,S,Se. I'm not saying that this is rigorous, just that its possible to do. My main point here, though, is to ask if you *really* need to bother with

[gmx-users] how to strip velocities out of a .gro file

Shay: that's a better idea than I had, thanks. Tsjerk: that's likely as fast as its ever going to get. this is great. I was initially worried that it would mangle the last line of the .gro in a triclinic box definition, but it seems to be ok. Thanks all, Chris. -- original message -- What

[gmx-users] how to strip velocities out of a .gro file

If you have a directory full of .gro files that contain velocities, and if you don't need those velocities, then you're taking up too much space on your drive. It's too bad, but trjconv -novel -f in.gro -o out.gro will still write the velocities to out.gro. Here's a small script to strip

[gmx-users] another pull-code question

Hi guys, I just wanted to chime in on the idea that how you perform the initial pulling to get structures isn't all that important because I strongly disagree and think that it is, in general, immensely important. OK, it's actually not important if we're talking about pulling two Na+

[gmx-users] another pull-code question

Sounds correct to me. One can use any method to generate the starting conformations. Some methods may yield equilibrium starting structures faster than other methods, but they are all ok in principle. Nevertheless, as with any simulations, one must ensure that care is taken to maintain

[gmx-users] another pull-code question

Dear Gavin: 1. Please use an informative title like pull_group0 moves unexpectedly so that those searching the list later can find it useful. 2. We're using Newton's equations, so equal and opposite forces are what you should expect. Why is there a problem is pull_group0 moves? Chris.

[gmx-users] Pull code

In addition to what everyone else has said, please note that pull_dim = N N Y is going to allow X and Y distance components to get as large/small as they will without any restraint. This may be what you want, but if you want a distance, but want it to be mostly in Z, then pull_dim = Y Y Y

[gmx-users] multiple time step

multiple timesteps are not possible as far as gromacs 4.0.7. NAMD can do this. -- original message -- Is it possible to carry out multiple time step molecular dynamics simulations in Gromacs 4.0. versions ? Could you please give me some information about this issue ? Thank you very much for

[gmx-users] different ref_t

Can you please supply gen_temp and also your pressure coupling values? Also, please supply the g_energy values that show the temperatures changing as you suggest (with accompanying timestep info). I'm fairly sure that what is happening is that you are simply seeing the nose-hoover

[gmx-users] multiple time step

I recall seeing something online about how gromacs developers have decided to focus on increasing the overall speed and allowing generally large timesteps (via e.g. angle constraints) vs. implementing multiple timestepping (no mailing list ref. sorry). I agree that this is not a logically

[gmx-users] g_anaeig -proj

Carla: Agreed that this can be confusing. What you seem to want can be obtained with g_anaeig -filt Nevertheless, What you get with -proj can also be very useful. For a very quick overview: -filt will output a .xtc file that contains only those motions that are along the selected EVs.

[gmx-users] standard state correction of delta G from a PMF

Dear Elio: I think I was pretty clear in my last email: If you still have trouble, then your next post should include things like I tried this... but I didn't understand this specific part to make it clear that you have put in the effort here. Otherwise, hopefully somebody else has the

[gmx-users] standard state correction of delta G from a PMF

Dear Elio: First, you need to convert your PMF to a free energy difference between states. That means defining a boundary between, for example, bound and unbound states. The integrate your PMF over the bound and unbound states to get two dG values, and their difference is your free

[gmx-users] grompp fatal error Unknown bond_atomtype

There's lots of information in the gromacs manual to show that the .atp file is not the only file that you must modify. My most important suggestion to you is that you should read the entire manual, possibly twice, before attempting to build new molecules. Gromacs manual, page 96: 5.3.1

[gmx-users] Energy miscalculation

Dear Thanasis: 8 posts on the same topic? I didn't even read them. If you want some help, I'd suggest that you start with a new subject line and post a single email containing all relevant information. You can see how it looks at the bottom of this list:

[gmx-users] umbrella sampling-Bimodal Histograms

Please clarify: Are doing SMD or are you doing US? If you're doing SMD then you should not be using WHAM and you should not really be able to generate any sampling histograms. Are the histograms that you are referring to population densities of the sampling along your reaction

[gmx-users] pull_pbcatom reporting strangely when set to 0

You're right, although I did not realize this at first. I got confused (again) by the global numbering. Regarding the off-by-one numbering, I can figure out what is meant there and that was not really my question. Thanks Berk, and sorry for the confusion. Chris. I coded this and I looked

[gmx-users] umbrella sampling-Bimodal Histograms

Take that replica on the left that shows a bimodal histogram. Now plot a time series of the displacement: x-axis = time and y-axis = displacement along reaction coord. Is it jumping back and forth between two regions of sampling? Probably not... more likely it starts near one maximum and

<    1   2   3   4   5   6   7   8   9   >