[gmx-users] Different results from identical tpr after MD

Dear Acoot: The idea of convergence is this: start a large number of simulations from different conformations, analyze some quantity over time in each simulation, and when the deviation of the average value of that quantity from each separate simulation is less than the time-variance with

[gmx-users] further discussion on the mdrun -append function

Dear Acoot: You should be able to answer this one yourself. Moreover, you are doing yourself a disservice by relying on the mailing list to do your work for you because you will eventually need to learn how to find answers to these things on your own. Please remember the following: 1. us

[gmx-users] on the Umbrella Sampling on-line tutorial

Dear Acoot: I'll reply to general topics, not to the tutorial in particular. If the opening is not large enough to allow the peptide to exit, then the surrounding protein will need to change its conformation to permit unbinding. This can happen, but you need (a) to have sufficiently long s

[gmx-users] How to compile the template.c when GMX is builded with cmake

Dear Users: I was previously able to compile template.c after I compiled gromacs with autoconf. I was unable to compile templae.c, however, I used cmake to compile gromacs. This is from gromacs-4.5.4. I tried "cmake ." in the template directory with no success: cmake .gpc-f102n084-$ cmake

[gmx-users] Not able to continue with Equilibration

I didn't follow this whole thread, but I sometimes need to turn off all constraints when doing minimization. In fact, for that reason I entirely stopped ever using restraints during energy minimization. In extreem cases, I have had success also by forcing the water to be flexible with a -DF

[gmx-users] Umbrella sampling along Radius of gyration

It is not clear to me how one would do this with MD. The only thing that I can think of doing in gromacs is to create a virtual particle that is placed at the center of the protein and then apply forces along the vector from this virtual atom to each of the Ca atoms. You would need to modif

[gmx-users] crazy temperatures

I disagree. What one is generally trying to obtain with elevated temperatures is enhanced sampling, not temperature-dependent properties. I believe that even TIP4P-EW is not very good at getting the properties of water correct at 600 K, temperatures that are commonly used during replica e

[gmx-users] Announcement: Large biomolecule benchmark report

You should absolutely publish this. it would be of great interest. You can mitigate your chances of running into problems with the overview by sending a version of the manuscript to the developers of each software and asking them to provide a short paragraph, each of which you could include

[gmx-users] intel grompp with pathscale mdrun

.12.1 = 3.467 ns/day pgi 11.8 = 3.092 ns/day pgi 11.8 with -tp istanbul -fast = 3.156 ns/day Again, thank you, Chris. -- original message -- As far as compilation hanging...maybe hand-compile that .o with less aggressive optimization flags, then try "make" again? MZ On Tue, Dec 6, 2011 at

[gmx-users] intel grompp with pathscale mdrun

Dear users: can I use a .tpr file created with an intel icc compilation of grompp and then do mdrun under a pathscale compilation of mdrun ? (same version of gromacs) I'm wondering if there would be some strange behaviour. It seems like it should be ok, but I wanted to be sure. I ask beca

[gmx-users] Half double pair list method in GROMACS [update]

What you have done seems alright. I didn't look closely enough to be sure though. One of the good things about this method is that you can easily test it yourself. To do this, create two different .gro files, one containing the atoms from one ff and the other containing the other atoms. For eac

[gmx-users] Failed to lock .log. Already running simulation?

Dear Users: I have 50 simulations that are all the same, except with different random seeds for velocities. All were running fine for 24 hours. I canceled the running jobs and resubmitted them as part of beta testing a new cluster. All 50 started. I then canceled one of these jobs soon af

[gmx-users] compiling with the PGI compiler

Dear Szilárd: Thank you for the advice. I made a mistake when I said that I was using new Xeons. The new cluster is actually composed of AMD Opteron Magny-cours 6172 (12-cores at 2.1 or 2.2 GHz grouped as 24-cores per node). It was because of the AMD architecture that I was trying with th

[gmx-users] compiling with the pathscale compiler hangs on gmx_rms.c.o

Dear users: My compilation with the pathscale compiler hangs for over an hour on the gmx_rms.c.o file (or perhaps the one that comes next). [ 83%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_principal.c.o [ 84%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_polystat.c.o [ 84%

[gmx-users] compiling with the PGI compiler

I am using a new cluster of Xeons and, to get the most efficient compilation, I have compiled gromacs-4.5.4 separately with the intel, pathscale, and pgi compilers. With the pgi compiler, I am most concerned about this floating point overflow warning: ... [ 19%] Building C object src/gmxlib/

[gmx-users] diffusion of the water at the micelle surface

Well, the positive way of looking at this is that it appears that nobody has ever done it before. If somebody has done it (in charmm for instance) then you might be able to convert the format of your .xtc and use their tools to analyze it. Good luck, Chris. -- original message -- Thank yo

[gmx-users] to gro or not to gro

1. why repeat the calculations? If you're talking about simulations then there is no need to repeat them due to this. You will get different answers with the same starting coordinates if you simply change the initial velocities. If you're talking about instantaneous energy calculations then

[gmx-users] to gro or not to gro

There is rounding because of angstroms vs nanometers and both files maintain 3 decimal places (see below). The intention of pdb2gmx is not to get a .gro , but to get a .top or .itp file. I see your point, but I don't think it matters. If you really need that precision, then I'd think that

[gmx-users] diffusion of the water at the micelle surface

When people do this for lipid bilayers, they compute depth-dependent diffusion profiles (often diffusion is computed separately for lateral diffusion and diffusion along the bilayer normal). Sounds like you might do something similar. I doubt that the standard gromacs tools will do this for

[gmx-users] to gro or not to gro

It's more useful if you provide more information. What was the .pdb file (can I download it from the pdb databank?) was there water? what version of gromacs? was it compiled in double or single precision? what were your mdp parameters? -- original message -- There is something not quite ri

[gmx-users] calculating the pmf in constrained force simulations

Do you mean that you do constrained position simulations and want to know how to process the force? If so, read about thermodynamic integration (TI). I mostly work with US and position restraints, but for absolute constraints I believe that you should take the average force at each constrai

[gmx-users] Charged wall

You could create an atomistic charged wall by placing atoms in a plane or grid and using position restraints or freeze groups to keep them in place. You could them use the pull code to restrain part of the protein relative to an atom(s) in this atomistic wall. You could obtain your desired

[gmx-users] lipid bilayer and umbrella sampling

If you add position restraints to your DPPC molecules, then you are changing your effective order parameter. The PMF for the solute along the normal to a restrained bilayer will have a different shape than a PMF for the solute along the normal to an urestrained bilayer. Whether or not this is a

[gmx-users] umbrella sampling with "pull=constraint"

Dear Vijay: Can you please provide evidence for your claim that the harmonic potential is not applied properly, since you may decide to use pull=umbrella once you have set that up correctly. Importantly, movement out of the unit-cell is not a problem, as discussed a lot on this list. Neve

[gmx-users] source of opls Mg2+ parameters?

Thank you Tom! Aqvist_A12 = sqrt(gromacs_C12*10^12/4.184) Aqvist_A6 = sqrt(gromacs_C6*10^6/4.184) (equation verified based on the SPC water oxygen parameters, also listed in Aqvist). This reference (Aqvist, J (1990) J. Phys. Chem., 94 (21), pp 8021?8024) should probably be noted somewhere

[gmx-users] source of opls Mg2+ parameters?

Dear users: does anybody know where the OPLS magnesium parameters are from? As far as I can tell, they are not in Jorgensen 1996 or Kaminski 2001, In spite of the fact that many simulation studies reference these papers for their magnesium opls parameters. In fact, I do not think that the

[gmx-users] umbrella sampling convergence

The criteria are the same for any type of simulation. Generally, you must show that, as far as you can tell, the values that you derive are not going to change if you run the simulation a lot longer. Different quantities converge at different rates, so ideally you should check them all inde

[gmx-users] Mismatching in Bergers DMPC bilayer lipid topology

Dear James: Next time, please specify exactly what you did in enough detail for somebody else to reproduce it, much as in a manuscript. e.g. there is no "dmpc.gro" in that website. I can guess what you did, but that is not ideal. I took a look at the files that I suppose you used and the

[gmx-users] umbrella sampling

You need to evaluate convergence yourself for any simulation. I suggest doing the whole thing twice (or more) with different starting conformations. Also, look at the PMF from block averaging (generate one PMF from the 0-2 ns data, another from the 2-4 ns data, and so on) and see if there i

[gmx-users] RE:How to change the screen's output frequency?

Speaking of which, I think that all programs should by default list -hidden when they are run with -h so that users are aware that there are hidden options and know how to access them. The -h output could clearly indicate that such options are not fully tested, etc. Chris. Justin A. Lemkul

[gmx-users] pull code problem: between protofilaments

Dear Shilpi: Can you use something like this? pull = umbrella pull_geometry= position pull_dim = N N Y pull_vec1= 0 0 0 pull_start = no pull_ngroups = 1 pull_group0 = PRO-1 pull_pbcatom0

[gmx-users] check point file corrupted - umbrella sampling

, i haven't outputted md.log file for each window. Kind Regards, Chetan. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Chris Neale [chris.ne...@utoronto.ca] Sent: 19 September 2011 17:59 To: gmx-users@gromac

[gmx-users] check point file corrupted - umbrella sampling

I have used tpbconv -until to extend a US simulation without error, and I assume that tpbconv -extend is also fine for US simulations. 1. Are you using the same version of gromacs mdrun as you used to produce your .cpt file initially? 2. what happens when you run gmxcheck on the .cpt file? 3.

[gmx-users] Twin-range cut-off

I believe the first mention of a twin-range cutoff was: H. J. C. Berendsen in J. Hermans (Ed.): Molecular Dynamics and Protein Structure, Polycrystal Book Service, Western Springs, IL, USA 1985. 18 There is also a nice discussion of it here: W.F. van Gunsteren and H.J.C. Berendsen. Agnew. Ch

[gmx-users] atom type OXT

You still haven't provided all of the relevant information. For example: what ff are you using? But please don't just sent that information now... better for you to read about how to develop a good post and next time be suer to include enough information that we could reproduce the problem

[gmx-users] Constraints not working in pull code (sometimes, sometimes not)

sly, while the errors in free energy differences on DOPC were rather small, the errors on octanol were strangely high. We have prepared smaller slabs (as Chris Neale suggested) of octanol with comparable size of box and we have also tried to analyze the position of centres either via pullx.xvg provid

[gmx-users] will united-atom POPC forcefield mater in pH 4

Zhijun: This is a question for the gmx-users list, so I will address it there. Please keep this type of question on the users list. 1.Are hydrogen ion H+ probably bind to POPC's phosphate O atom when I randomly assign it? That sounds a lot like something that you can test. Na+ ions do not

[gmx-users] Half double pair list method in GROMACS

I think it's reasonable for you to post this on-list. It's not your method and you got help here and somebody else might want the same help in the future. Chris. -- original message -- ABEL Stephane 175950 Stephane.ABEL at cea.fr Thu Sep 1 22:22:27 CEST 2011 * Previous message: [gmx-us

[gmx-users] GROMACS 4.5.4 keep crashing all the time

That seems possible Mark. I had actually assumed that Itamar extracted a .gro from the 4.0.7 simulations and created a new .tpr with 4.5.4 grompp. If that was the case, then I would still be surprised that it had instability problems. One sees a lot of charmm papers where people do slow hea

[gmx-users] Half double pair list method in GROMACS

It's a typo, but it's in the discussion and not in the "do this" part of the method so I decided not to mention it. I don't see another question in this post, so I hope that you have figured things out. Note that I have never tested the exact implementation that I suggested in that April em

[gmx-users] order parameter

In addition to Justin's comment about g_order being incorrect for unsaturated carbons, you won't ever get numerical agreement with g_order, even for saturated carbons, because g_order does not use your explicit hydrogens. g_order uses the positions of the carbons to rebuild the hydrogen pos

[gmx-users] half double pair list method in GROMACS

Dear Stephane: We discussed this in April: http://lists.gromacs.org/pipermail/gmx-users/2011-April/060839.html At that time I also provided a method for you to verify your files (and the method in general). It is possible for you to answer your gen-pairs question by looking into the manua

[gmx-users] GROMACS 4.5.4 keep crashing all the time

That all makes sense Tsjerk. I wonder if mdrun terminations based on LINCS warnings should come with an additional message to explain that one may try running for a while with nstpcouple=1. Also, I'm still a little curious about a question that Itamar asked a few posts ago: "If this is

[gmx-users] Non-zero total charge

6.30e+01 = 63 -- original message -- My system had a no zero total charge: System has non-zero total charge: 6.30e+01 I used genion to neutralize the system by adding 6 CL ions. After updating the topology file, the system still seems to have the same problem. It still has a non-zer

[gmx-users] GROMACS 4.5.4 keep crashing all the time

I am glad that the pressure coupling intervals have been identified as a source of instability for poorly equilibrated systems as I was unaware of that. Still, the fact that the SD integrator also solves the problem also suggests that this is simply a poorly equilibrated system. I am not su

[gmx-users] GROMACS 4.5.4 keep crashing all the time

Itamar: We really are trying to help. I think that perhaps you don't grasp how difficult it is to help without being able to access the simulation directly. Therefore we have ideas and we ask you to do specific things that are going to move us toward a solution, either by finding answers

[gmx-users] order parameter

Dear Ramya: Are you simulating all-atom lipids (with explicit hydrogen atoms on the acyl chain)? If not, then you missed a step in your description of what you have done (g_order, for example, ignores explicit hydrogen atoms so that it can act on united atom lipids). Not sure why PBC woul

[gmx-users] g_wham issue

Please provide very much more information. Unless somebody has run into the exact thing that you are describing it is currently impossible for us to help you. One thing I can suggest now is to construct histograms of the sampling from the coord.xvg files yourself with some scripting and plo

[gmx-users] Free Energy Integrator Selection

Try running for longer and look at the convergence of the temperatures over time. I suspect that what you are reporting is actually just statistical noise. I am not sure about using the sd integrator and defining multiple temperature coupling groups... If you define the same temperature for

[gmx-users] Re: parallel job crash for large system

Your density seems to be about 70% of what I would expect. Are you sure that this is not just a normal case of a poorly equilibrated system crashing? That matches with what you say about the density growing (although perhaps it has more to do with poor equilibration than with mixing, as you

[gmx-users] wibke.sudholt spam needs to stop

That's 9 times in the last 20 days that a single user has hit the list with an auto-reply that seems a lot like an advertisement. Can somebody please ban this user? The most recent example: http://lists.gromacs.org/pipermail/gmx-users/2011-August/063991.html -- gmx-users mailing listgmx-

[gmx-users] problem with g_density -center

g_density is not compatible with constant pressure simulations. You must modify it to construct the bins outward from the bilayer center when doing NPT: http://lists.gromacs.org/pipermail/gmx-users/2010-November/055651.html Further, trjconv -center is misleading. I actually lost a lot of tim

[gmx-users] more than 100% CPU

Slightly off-topic, but for all but the smallest systems, I get a further 10% efficiency by running a 16-process mpi job on an 8-core machine. I suspect that the story is the same with threads. Thus, on a 16-core node, you could try starting 32 threads. Note that this will report a 2x large

[gmx-users] GROMACS 4.5.4 keep crashing all the time

OK, here's my last few ideas: 1. Please try to repeat this with gen_vel set to the same value as your temperature coupling 2. Can you reproduce this in serial? 3. Can you reproduce this with the sd integrator? 4. Can you reproduce this with a simpler system? protein in vacuum or just wate

[gmx-users] GROMACS 4.5.4 keep crashing all the time

run an EM with flexible water. I often find that this is the only way to get a stable system. 500 steps of steep with define=-DFLEXIBLE (or different depending on your water model I think) should be enough. Chris. Hi Chris and Justin, On 18/08/2011, at 9:36 AM, Justin A. Lemkul wrote: c

[gmx-users] GROMACS 4.5.4 keep crashing all the time.

You'll need to provide a much better report than this if you want to receive any useful help. Copy and paste the exact commands of what you did Copy and paste the exact log file and error messages Do this for 4.0.7 and 4.5.4, for which I trust that you have been using exactly identical test

[gmx-users] suggestion that mdrun should ensure npme < the number of processes

Currently, gromacs4.5.4 gives a segfault if one runs mpirun -np 8 mdrun_mpi -npme 120 with no warning of the source of the problem. Obviously npme>nnodes is a bad setup, but a check would be nice. Thank you, Chris. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/ma

[gmx-users] vsites with NAC and opls

This is fixed, just posting for posterity. If one wants to run pdb2gmx with -vsites hydrogens on gromacs 4.5.4 or 4.0.7 while using the oplss ff, there is the error message: Fatal error: Can't find dummy mass for type opls_242 bonded to type opls_238 in the virtual site database (.vsd files

[gmx-users] Constraints not working in pull code (sometimes, sometimes not)

Dear Krapnik: 1. please make the test cases identical, that means doing a simulation that you may not really be interested in so that the solutes are the same for both lipid and octane. It also means setting the displacements to similar values in my opinion (because perhaps the problem is

[gmx-users] Constraints not working in pull code (sometimes, sometimes not)

I agree that Justin is probably correct, although constraints should technically work just fine with a highly dynamic reference group. Any problems should show up as the system blowing up, but not in correctly setting the position. I think that the problems can arise, however, when you have

[gmx-users] spatial distribution function in a binary solvent mixture

Here's the totally wasteful way for you to get what you want: 1. for each molecule in type A: trjorder everything around that molecule and output only the closest N atoms of type A and the closest M atoms of type B. Ensure that the coordinate order is: your central molecule of type A is fir

[gmx-users] spatial distribution function in a binary solvent mixture

I think that you have a misconception about what g_spatial does. For a system with many type A and many type B, you need to average over all of one type as the central solute to compute an rdf, and perhaps that is what you want for your sdf. g_spatial, however, does not do any fitting. g_sd

[gmx-users] umbrella sampling

I've never actually reweighted with F-values. These are the values by which the component PMFs are shifted during WHAM after debiasing the umbrella potentials. Look at equations 6 and 7 in "The multicanonical weighted histogram analysis method for the free-energy landscape along structural

[gmx-users] umbrella sampling

format your data for 2D-WHAM with 1D being the distance and the 2nd-D being your other coordinate of interest. Specify a value of zero for the force constants for your 2nd-D. Run 2D-WHAM. Boltzmann project the 2D PMF onto your 2nd-D. I think you can also do essentially the same thing by re-

[gmx-users] large error bars in PMF

I see now what you mean. As it happens, I doubt that this would have caused the problem since no force was applied on X and Y dimensions, so it would require that there was a PBC-based distance degeneracy along Z, although this is of course possible and hopefully Rebecca will answer this pa

[gmx-users] large error bars in PMF

I don't see why the box-type makes any difference whatsoever. It is possible that if you use a rhombic dodecahedron, you may reduce the system size, thus simulate more ns/day, thus converge faster, but that should be the only effect. I would be interested to hear more from Justin about how

[gmx-users] g_msd bug

600 GB of memory? I highly doubt that you have that much memory available. Are you sure that this is not a typo? Can you please post evidence that you have >=600 GB of memory available? It is common for clusters to disallow an individual process from using >10% of the total memory on a head

[gmx-users] gromacs 2.1

In the middle of my last post, it should have stated: "I moved the **include** directory into src/ and that solved the error messages that I was obtaining, but now make errors with:" Sorry for the confusion, Chris. Quoting chris.ne...@utoronto.ca: Thank you Rossen and Roland. I was able to o

[gmx-users] gromacs 2.1

Thank you Rossen and Roland. I was able to obtain the source but not compile it. It would be appreciated if you can offer any suggestions. I obtained gromacs via: git clone git://git.gromacs.org/gromacs.git git checkout release-2-0-01 But I can not compile it. When I cd src and run make or

[gmx-users] pulling code

Dear Adam: I have a number of questions listed below. But first, I think it would be useful if you explain exactly what you want to accomplish and how you tried to do this with non-modified code and what problem you ran into that caused you to modify the code. After you outline that, plea

[gmx-users] T->A mutation for a dimer protein

Dear Lishan: First, it would be great to see some evidence that you have tried to do this yourself before posting. Your "I think" makes it a possible waste of time for us to suggest a resolution to a problem that may or may not exist. Second, if indeed it is a problem, perhaps you could u

[gmx-users] Timing variability

Dear Users: Has anybody else looked at simulation speed (ns/day) over the segments of long runs? I always benchmark and optimize my systems carefully, but it was only recently that I realized how much variability I am obtaining over long runs. Perhaps this is specific to my cluster, which

[gmx-users] restraints in PMF (Justin's tutorial)

Actually, this depends on what you are trying to achieve. If you simply want to obtain the standard binding free energy, and somehow you know that the bound state is represented by your umbrella at dist=0 (via a crystal structure, for example), then using additional restraints is common, ac

[gmx-users] Programs to add residues

Try "Loopy". You can get it to build termini in addition to loops. http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:Loopy Nevertheless, I'd suggest simply omitting that part of the protein and capping your new terminus to remove the charge. You will have more difficulties conve

[gmx-users] is lincs used with virtual hydrogens?

Thank you Mark, I really appreciate it. -- original message -- On 20/06/2011 1:23 AM, chris.neale at utoronto.ca wrote: Dear Mark: Now I am confused. Your first post indicated that P-LINCS did the angle constraints. But here you indicate that the v-site algorithm does it. No... my second

[gmx-users] is lincs used with virtual hydrogens?

Dear Mark: Now I am confused. Your first post indicated that P-LINCS did the angle constraints. But here you indicate that the v-site algorithm does it. This is probably because my first post was incomplete about the method that I used. Can you please confirm my current understanding? Th

[gmx-users] is lincs used with virtual hydrogens?

Thank you Roland. I did use: constraints = all-bonds lincs-iter = 1 lincs-order = 6 constraint_algorithm = lincs From looking at the manual, I figured that angle and bond constraints would all be done by LINCS if I had done (A): pdb2gmx -vsite none constraints = h-angles (a combination t

[gmx-users] is lincs used with virtual hydrogens?

Dear Users: If I create the topology of a peptide like this: pdb2gmx -f protein.gro -vsite hydrogens And then simulate it in vacuum, is lincs used at all? I believe that it is, as if I use a timestep that is too large then I get LINCS warnings about angles rotating more than 30 degrees, but

[gmx-users] gmx4.5.4 genion problem: No line with moleculetype 'SOL' found

For the quick fix: 1. run genion on your topology that does work. Look at this to see the format of the ion atom and residue names 2. Pick a few waters in the structure containing the ligand and replace the OW by the ion and remove the hydrogens, then fix the number of atoms on the second

[gmx-users] g_hbond

From g_hbond -h "OH and NH groups are regarded as donors, O is an acceptor always, N is an acceptor by default, but this can be switched using -nitacc. Dummy hydrogen atoms are assumed to be connected to the first preceding non-hydrogen atom." The two groups are to find hbonds between gro

[gmx-users] Can't unfold the protein

Dear Hsin-Lin: I am no expert in this area. I am just saying that if you get densities that are way too low in NPT, then you might alleviate this problem with NVT. In fact, I would personally do this in vacuum without pbc and use the sd integrator. Then you can sample extended conformatio

[gmx-users] Can't unfold the protein

Dear Hsin-Lin: The first thing that comes to mind is using very high temperatures with NVT. Obtaining the desired denatured state is a complex challenge, but you might try this paper: Phys. Rev. Lett. 93, 238105 (2004) Reversible Temperature and Pressure Denaturation of a Protein Fragment:

[gmx-users] g_dist

Dear Nilesh: You don't seem to have made any progress since Mark gave you some reading hints. Your best chance to get a useful response follows the general form: 1. I want to do A. 2. I tried method B, here are the exact commands that I used (copy and paste) 3. With that method, I obtain C

[gmx-users] g_density

Dear Matthias: Did you run trjconv -center -pbc mol at some point before running g_density? With pbc, there are multiple ways to put the center of a system at the center of the box. This can lead to having the water slab in the center of the unit cell and the bilayer on the top and bottom

[gmx-users] centering a bilayer at a cartesian coordinate

I solved it. It was my own error to assume that trjconv -center centers the COM. Actually, it centers the value of (min+max)/2 in each dimension. I can modify trjconv locally to do what I want. Thank you, Chris. static void center_x(int ecenter,rvec x[],matrix box,int n,int nc,atom_id ci[

[gmx-users] centering a bilayer at a cartesian coordinate

Dear users: I am trying to process a trajectory so that a group of molecules has their center of mass at a constant position in Cartesian space. I have not been able to figure out how to do this. The reason that I would like this is that I have conducted umbrella sampling of a solute alon

[gmx-users] Question about umbrella sampling through a nanotube

Unfortunately, I don't think that there is any way to use this data (and only this data) to derive the PMF along z. The way that you did your US, the PMF along z is convoluted with xy motion. You can get the PMF along the reaction coordinate that you actually used (XYZ) using standard WHAM

[gmx-users] Gradually increasing the force constant during restrained MD runs

Dear Aditi: you can do this by scripting gromacs to run in short segments, modifying the force constant for each run. e.g.: #!/bin/bash for((i=1;i<=100; i++)); do let "j=i-1" grompp -f ${i}.mdp -p ${i}.top -f ${j}.gro -o ${i}.tpr mdrun -deffnm ${i} done You only need to use some more s

[gmx-users] gromacs 2.1

Dear users: Does anybody have the source code for gromacs version 2.1? I would like to check the original source of g_order, but only versions 3.0 and above are available on the gromacs website. Thank you, Chris. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/m

[gmx-users] Calculation of unsaturated deuterium order parameters for POPC

I have patched g_order version 4.5.4 to compute the order parameters in a different way. Despite trying, I don't understand the original g_order implementation. In the version that I am providing, the hydrogens are explicitly built and the coordinates of these hydrogens are output to stdout

[gmx-users] Calculation of unsaturated deuterium order parameters for POPC

Dear Thomas: I agree with your conclusions about g_order. My usage of the Berger POPC lipids in combination with the g_order command (as per the instructions in http://www.gromacs.org/Documentation/Gromacs_Utilities/g_order ) yields order parameters of 0.193 and 0.051 for the first and sec

[gmx-users] Why does the -append option exist?

Dear Dimitar: to me, your posts have indeed appeared very aggressive. So much so that there are probably many people who can help who have decided not to bother due to what they perceive your tone to be. On to the problem at hand: I agree with the previous suggestion that you may have som

[gmx-users] binaries for mac os x 10.6

Dear Users: Does somebody have a set of gromacs binaries for mac os X 10.6.7 that they can post somewhere (perhaps in http://www.gromacs.org/Downloads/User_contributions/Gromacs_binaries)? Macbook Air 3.1 Version 10.6.7 1.4 GHz Intel Core 2 Duo 2 GB 1067 MHz DDR3 SMC version 1.67f3 I am t

[gmx-users] problem during energy minimization

1. you're not doing energy minimization as your title suggests, please use a better title: integrator = md 2. generally, when you have a problem it is useful to try to simplify the system (e.g. get rid of those tables) and try to reproduce the problem with the simplest system possible be

[gmx-users] How to get angle distribution between two tyrosine stacking residues

1. Determine some mathematical calculation that you want to apply to some atoms. 2. make a .ndx group that includes all of those atoms 3. Run g_traj -ox to output the coordinates of those atoms 4. Apply your mathematical calculation using awk. -- original message -- Can anyone tell how to calc

[gmx-users] Rigid structure and flexible structure present in sing system

If I read between the lines correctly, you know how to do this in gromacs, but you wish that you got a big speedup from freezing most of the atoms in your system. If that is the case, then I think that gromacs can not help you in its current form. Therefore, I suggest that you try the Charm

[gmx-users] tabulated potential energy=nan for r=0 nm and charged atoms

Dear users: with assistance from Berk on the developers list, I am posting a work-around to this issue. the nonbonded interactions calculate the nonbonded distance, r, using the gmx_invsqrt function. Thus, the optimized kernel from 4.5.4 and 4.0.7 both give nan when two charges occupy the

[gmx-users] beware gen-vel=no

Regarding gen-vel=no as discussed here: http://lists.gromacs.org/pipermail/gmx-users/2011-May/061151.html I would caution against the general use of gen-vel=no and then coupling to a temperature of 300 K with the Berendsen thermostat. One problem that can arise is concerted unfolding. Tempera

[gmx-users] tabulated potential energy=nan for r=0 nm and charged atoms

Dear Users: I am trying to work with tabulated potentials for the first time. I would like to allow 2 charges to be at the same spot. Imagine taking a sodium and chloride ion and removing the LJ entirely and I want the system to evaluate energies correctly and be stable during the simulat

[gmx-users] constraints

generally, look at mdout.mdp from grompp -- original message -- In my input file if I don't specify "constraints" then What is default constraints=none constraints=all bonds NIlesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Ple

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