[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] 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] 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] 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] 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] 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] 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] 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?

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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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

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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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

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] 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] 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

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] 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

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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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 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] 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] 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] 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] 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] 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] 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] 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] 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

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] 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] 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] 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] 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

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] 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] 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] 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] 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] popc

You are experiencing problems because popc is not a protein and pdb2gmx is currently only set up for proteins. More importantly, you already have popc.itp so you don't need to run pdb2gmx on it. I suggest that you read the manual more closely about setting up a simulation and clarify your

[gmx-users] OPLS-FF

If I understand correctly, the rebuilt residues do not connect to each side of the gap correctly? You state about gaps: "actually it shouldn't appear after minimisation.", but it is not necessarily true that EM is capable of bringing the residues properly close together. I think you mean th

[gmx-users] Re: Informatin about Force field for Protein in POPC

Please keep this on the mailing list. I use OPLS + tip4p for protein in water, then I use the Berger lipids downloaded from Peter Tieleman's website using some special considerations for scaling of the 1-4 interactions. You can find some of my posts on that topic via searching for opls and ber

[gmx-users] combining the OPLS-AA forcefield with the Berger lipids

To wrap up combination of the OPLS-AA forcefield with the Berger lipids, I have posted a detailed description of the motivation, method, and testing. Much of the methods there will be used in a paper at some point in time so please do not copy the text directly for your own use. http://www.pom

[gmx-users] OPLS-AA/L

Check the archives. I posted a summary of one possible solution less than 8 hours ago. You will receive more assistance if you demonstrate that you are trying to help yourself. If you still don't find the answer that you are looking for then you need to be *way* more detailed in your questi

[gmx-users] OPLS-AA/L

Yes, the LO LO in atom type should be as Justin has mentioned. Sudheer, please note that the original post that you quote below actually includes an example for LO LO "LO LO 115.9994 0.000 A2.96000e-01 8.87864e-01" Also note that similar information is available i

[gmx-users] How to modify H atom type from opls_369 to match H expected by popc.itp

There is no need to post twice, I saw your first post. Your level of questions indicates that you still do not understand the topology file format. It is essential that you understand exactly how it works and what is going on or else you are more likely to have errors in your simulation. I am h

[gmx-users] Problem with lipid simulations

Where is lipid.itp and your other forcefield files. Check that they are identical between your two clusters. This appears to be a problem with files and not with the installation. If you can't figure it out, you will need to post your topology at the very least and also post 'grep LO ffopls

[gmx-users] continuation run in parallel with shuffle and, sort option

While the previously posted script seems like a valid approach, the usefulness of -sort depends entirely on how long your trajectory is. If you only sort once at the beginning, then after <<10ns your waters will be mostly redistributed and I think that you will have totally lost the benifits of

[gmx-users] continuation run in parallel with shuffle and sort option

Thanks a lot for your suggestion. I wanted to calculate lateral diffusion co-efficient for lipid, so it needs a long run. I understand I should give more time on making this working. I have already downloaded g_desort.c, and was successful upto some steps, but not the whole. If I get doubts furthe

[gmx-users] hydrogen bonds of peptide with lipids

Are you using united atom lipids? If so, you may want to reconsider attempting this. If not, you'll be more likely to get further assistance if you provide quite a bit more information and demonstrate that you invested some time trying to solve this. -- original message -- Yes, I looked in

[gmx-users] 3.3.2 -b option not functioning as expected

Hello, I find that trjconv and g_order 3.3.2 don't properly find the frame to which I would like to seek via -b. I initially discovered this based on the output to the command line from g_order about which frame is being processed, and I have further confirmed that the incorrect frame is actu

[gmx-users] Lipid forcefield to use with TIP5P/OPLSaa

I use tip4p/opls/berger combination and it works well for me. I have never used tip5p. I suggest that you build your membrane and run one control simulation (sounds like you would lean toward using spc for this) and then one simulation with tip5p. Check order parameters and area per lipid while us

[gmx-users] 3.3.2 -b option not functioning as expected

Indeed, 3.3.3 works well. Thanks David and Berk. Chris. Chris Neale wrote: / Hello, />/ />/ I find that trjconv and g_order 3.3.2 don't properly find the frame to />/ which I would like to seek via -b. I initially discovered this based on />/ the output to the command

[gmx-users] request for default word-wrap on the mailing list

Is it possible for the moderators to change some setting that would automatically word-wrap all posts on the mailing list archive? Many of my posts end up spanning more than the horizontal space on one screen when viewed from the mailing list archive. I try to remember to add hard returns on each

[gmx-users] Entropy correction in PMF

That sentence could definitely use some massaging. Try this: Whether one needs to correct for this contribution depends on what the pmf should represent. When one wants to pull a substrate into a protein, this entropic term indeed contributes to the work to get the substrate into the protein. Thi

[gmx-users] area per lipid

Probably you would benefit from putting down your simulation and spending the next week reading. search the literature for membrane simulations in the absence of proteins, read it, and duplicate the tests for simulations matching experiment that you see. --original message -- Hi I have re

[gmx-users] combining differently-generated force-fields

I don't have a problem, per se, but would like to discuss the problems that may, or may not, arise when mixing force fields. It is clear to me why one would not want to calculate the free energy of binding for two proteins, one using the amber ff and the other using the opls ff; also it is

[gmx-users] Re: combining differently-generated force-fields

Thanks Soo Mei, that might be interesting. I couldn't access it either. I think it is a book (http://www.springer.com/series/7651) MacKerell's website indicates that it is not yet in press, although I am not sure how recently that was updated: Guvench, O. and MacKerell, A.D., Jr., ?Comparis

[gmx-users] benchmark: buying a new cluster

To some extent, it depends on your interconnect and the number of atoms in the simulations that you will be doing. If you are using gigabit ethernet, then you may not scale very well beyond 8 cores on these dual node quad cores and so there is an argument to be made for 10% faster. However, if you

[gmx-users] bilayer DMPC

Please post again, this time turn off your html formatting in your email. It is too difficult for me to read with all of the   characters. Also, please be more explicit about what the problem is. Is your area per lipid too small? It seems that way, but I did not use DMPC myself. I use POP

[gmx-users] Re: gmx-users Digest, Vol 49, Issue 53 bilayer area problem

1. You really must figure out your email issue. Go to http://www.gromacs.org/pipermail/gmx-users/2008-May/034065.html to see what some of us have to wade through to assist you. 2. Avoid changing your subject line when continuing a discussion 3. Did you address Marks comment about " define =

[gmx-users] Force field parameters in water or in vacuum?

Please don't post to the users list and the developers list simultaneously with the same question. I think this is more appropriately a users list question. I guess if you also get a reply on the developers list then it pays to post to both, but the idea is to put it only in one space. H

[gmx-users] small typo in ions.itp: LI+ atom is NA

I noticed this typo in ions.itp under the FF_OPLS section. It appears to have been present at least from 3.2.1 to 3.3.3 (the atom name for LI+ is NA) [ moleculetype ] ; molname nrexcl LI+ 1 [ atoms ] ; idat type res nr residu name at name cg nr charge ma

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