[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] 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. Separat

[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 ti

[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] 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 energy

[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 tr

[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 a

[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 coordinate?

[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: http://lists.gromacs.org/pipermail

[gmx-users] Query on WHAM analysis

loc_win_min is the center of restraint spring is the force constant in kcal/mol (1000kJ/mol/nm^2 /4.184 = x kcal/mol/nm^2) You should probably read the manual again, this stuff is all there. I'll not answer any further questions on this as (1) it's in Alan's manual, and (2) this list is not

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

Dear gromacs users: I am confused (again) about pull_pbcatom0. From this analysis, I am questioning if the pbcatom reported from grompp and in the top of the .log file is numerically defined *within* a group or in the context of the entire .gro file. Either way, I think that I have conclu

[gmx-users] Enough hydration of the channel

Determining how many waters is sufficient is a tough problem, try successive runs of option #3, below. As for the simpler topic of getting more hydration: 1. If the issue is simply getting the channel hydrated enough to overcome some transition from dry to wet, then run a neat water box od

[gmx-users] Energy minimization: problems with ramachanrad score

This does not imply that less EM is better than more EM. It implies that the native structure is not necessarily in an absolute energy minimum according to our FF's. This is certainly true. We could take the point of view that when an experimentalist refers to as a "native structure" is act

[gmx-users] How to view evolution of secondary structure in a trajectory?

http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/sscache/ -- original message -- Hi, I am trying -with no avail- to have a way to view a movie of a GROMACS trajectory with the secondary structure being updated automatically frame by frame (that is, changing colour and/or appearance

[gmx-users] Disk Space

a question like "is this much really enough?" is impossible for me to answer. I suggest that you look at the autocorrelation times of your observables and perhaps (very likely actually) you will realize that you don't need to save nearly as often as you are saving. Also, read the manual abo

[gmx-users] Disk Space

Dear Rob: To answer your question: just set up your run with nsteps for 5 ns, run mdrun, and then use tpbconv -until. A simpler option is to set it up to run 20 ns, but use -maxh to limit it to an amount of runtime that you pre-calculate to be similar to 5 ns of simulation. HOWEVER: You

[gmx-users] PMF in vacuum and pull direction

Dear Eudes: Thanks for working with me on this one! What you are getting is actually what you are asking for in your .mdp file. You restrain the Z-projection of the displacement, but do not affect the X and Y components of the displacement with pull_dim = N N Y. If you want to pull with s

[gmx-users] PMF in vacuum and pull direction

Dear Eudes: This is better, but I'm afraid that I'm going to have to insist on getting everything I asked for. Please see my previous message. Chris. -- original message -- Dear Chris, I'm so sorry for surperficial email. You are correct because in the previous message I forgot to mention t

[gmx-users] PMF in vacuum and pull direction

Dear Eudes: You can make my job a whole lot easier! First, please go back through all of the comments that I gave you last time and reply to them one by one. Did you do them? What did you see? Second, please include your new .mdp and some quantitative results to better explain what you see

[gmx-users] number of water molecules affects the PMF

It depends on how you generated your error bars and how different your two setups were other than different numbers of water. Xavier's suggestion to split the sampling in half and report each half to the list remains an important piece of data for us to have. Also, please don't reply to the

[gmx-users] Re: add missing atom(s)

I use a program called Loopy to build in missing backbone atoms and a program called SCWRL3 to add in missing sidechains. I'm not advocating these as better than other methods, just that they work for me. You'll need to do some reading for each though in order to be sure that you do it corr

[gmx-users] Solvation Free Energy Calculation

Dear Emanuel: We need you to be much more specific. 1. What link? 2. Even though it might be in the link, you should still provide us with a general protocol that you followed. Chris. -- original message -- I am using Gromacs to calculate solvation of free energy calculation. First I tri

[gmx-users] SPC/E water RDF

Dear Francisco: 1. gromacs already has an spce.itp file. Try using that one directly and see if your answer changes. If it does, then one file is in error. 2. the density of spc/e is not 1g/cc. First thing, you should try to reproduce an RDF from the literature for which you use exactly the

[gmx-users] add missing atom

While Mark's answer is entirely complete, I'll just add one more idea in case you don't know where to put the OG. 1. Go into your .gro file and change the SER to an ALA 2. pdb2gmx to place the hydrogens around the CB 3. EM 4a. Copy the EM output .gro file into 3 directories, and in each one o

[gmx-users] umbrella sampling

Dear Qian: Debiasing equations for this can be found by analogy to eq. 16 and 17 in the the original Torrie and Valleau US paper: "Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling". Alternatively, I used a simple method in doi:10.1016/j.cplett.20

[gmx-users] Negative pulling forces, periodic molecules

Read about the .mdp options pull_pbcatom0 and pull_pbcatom1 -- original message -- Hi everyone, I have a pulling code running on single machine with Gromacs 4.0.7 The systems composes of a surface, a protein and water I pull the protein from the terminal group on the surface laterally. With G

[gmx-users] Constraint causing system to explode

Dear Warren: I don't have your answer, but I'll point out that when you ask: "Is it possible that this is a problem that arises because of domain decomposition over multiple nodes" that you are probably the person in the best position to address this. 300ps should not take too long to sim

[gmx-users] PMF in vacuum

Dear Eudes: To answer your pbc vs no-pbc question, I suggest that you use pbc=no and set nstlist=0 rlist=0 rvdw=0 rcoulomb=0 so that you calculate all interactions in direct space with no cutoffs. ## Major comments that you should still investigate 1. There is no need to use a virtual atom,

[gmx-users] PMF in vacuum

Dear Eudes: Can you please elaborate on your description? What .mdp options are you using? What exactly do your curves look like (you can post pictures to photobucket or some other online service and link them here)? If you suspect that you are doing something wrong, then we need to under

[gmx-users] reproducibility of PMF plot with two different starting structures

Your run is not converged. You could (i) run more slowly, (ii) run lots of these non-equilibrium runs and treat them appropriately, or (iii) use an equilibrium method. In any event, I suggest that you begin by (iv) repeat the run for both poses with different random seeds to see how much of

[gmx-users] SMD pulling question

Dear Justin: I still disagree. I know it's a fine point, but I think it's important. The PMF would, I presume, be created by applying a relative position restraint along Z between the center of mass of a large ligand and the center of mass of a bilayer and slowly changing the relative positi

[gmx-users] SMD pulling question

I guess that I am missing something, but how would restraining the position of the bilayer COM in absolute space have any affect on anything at all? I certainly agree that one wants to observe if the membrane has been destabilized, but if so then I think the solution would be slower pulling

[gmx-users] PMF of ligand transport

iguration when I run umbrella sampling, will this pull_init value needs to change?(I suppose so, if its true how?) When it should be negative and positive? Could you please explain this. Thanks for your valuable time Thanks & Regards, Aswathy On Mon, May 10, 2010 at 9:55 PM, Chris Neale w

[gmx-users] non zero charge in topolgy

Your problem is here: 8 opls_158 1HEX C3 3 0.12 12.011 ; qtot 0.12 As for the other questions, I could answer them but I think that it would preclude you from pursuing the more useful solution: read the manual and read some papers and do some tutorials.

[gmx-users] PMF of ligand transport

Pick a small collection of backbone atoms near the center of your channel and use them as your reference group. Overcome the sign problem by optimal selection of pull options (see below). pull_pbcatom values should not be important if you select your groups as I suggest -- otherwise be sure to un

[gmx-users] PMF of ligand transport

Don't use a dummy particle for your PMF if you can avoid it and test it thoroughly if you must use it. In my own work, I have received what appears to be erroneous results when using a dummy atoms together with dihedral restraints and the pull code. In my case I was actually using a dummy atom

[gmx-users] PMF of ligand transport

Dear Aswathy: While not technically incorrect, it will make convergence much more difficult and is probably realistically incorrect given today's cpu power. But then again perhaps you have some particularly important reason to make that choice. In the absence of that, find some atom(s) th

[gmx-users] Re: PMF profile using g_wham with pull_geometry = distance for ion channel

Dear Tom: Your idea will work, but only for the one replica centered exactly at 0.0; the other ones will need to be rerun. But you really should not need to rerun very many replicas, unless I misunderstand your setup. The problem is this: if your center of restraint is close enough to 0.0

[gmx-users] Compiling Gromacs 4.0.7 on AIX 5.3

Dear Sebastien: Perhaps it's obvious, but can you confirm that you used the compilation options that I posted? My suggestion was not so much that you should try to compile 4.0.4 but that you should try the options that I posted. So if you used your original compilation commands with gromacs ve

[gmx-users] Compiling Gromacs 4.0.7 on AIX 5.3

This worked for me on AIX 5.3 for gromacs 4.0.4, I didn't try to compile any gromacs versions after that because we found that gromacs runs much better on Xeons and Opterons than it runs on power6's running AIX 5.3 If you have a problem specific to 4.0.7 (i.e. you can compile 4.0.4 alrigh

[gmx-users] Concerns with g_wham

I have been using g_wham, but I have a few questions that I can't find answers to online. When using WHAM, one does not need the forces between the pull groups to calculate the PMF, yet g_wham won't run without it. Is there a reason for this? I have never used g_wham, but g_wham -h (gromacs-4.

[gmx-users] two reference groups in pull code

Dear Bin: What you request is not currently possible with any distribution up to gmx-4.0.7 (I don't know if it is in the cvs). I have a modified version of gromacs-4.0.5 that will do this, but we are not distributing it yet. We may upload it in the future for incorporation into the main d

[gmx-users] Problem with g_density

1. Please include the actual commands that you used via copy and paste so that we can see *exactly* what you did. 2. Please include a snippit of the *actual* output identifying where the difference is that you mention here. 3. Note that g_density has some limitations, all related to volume

[gmx-users] Parallel pulling with Gromacs 4.0.7: COMM mode problem

Dear Aykut: 1. Did you see the log file message: "comm-mode angular will give incorrect results when the comm group partially crosses a periodic boundary" 2. You say "Actually you might be right about the domain decomposition", but it seems like you didn't run it on gmx 4 in serial or with p

[gmx-users] Parallel pulling with Gromacs 4.0.7: COMM mode problem

If you pull in G3 with AFM option, with your reference groups is the surface, in the output pull.pdo file what you will get is solute (pulled group) coordinates /wrt the surface... Yes. Can we see the data that you get as output in each case and tell us what the major difference is? the

[gmx-users] Parallel pulling with Gromacs 4.0.7: COMM mode problem

Correction: what you are actually doing is pulling your solute to the (X,Y) center of mass of your surface + (2.0 * 0.001/ps) nm in X + the initial center of mass distance in X and Y. -- original message -- Dear Aykut, Please give a more complete description of 1) the .mdp options and expec

[gmx-users] Parallel pulling with Gromacs 4.0.7: COMM mode problem

Dear Aykut, Please give a more complete description of 1) the .mdp options and expected behaviour that you get with gmx 3.3.3 on a single core and 2) the .mdp options and difference that you get with gmx 4.0.7 in parallel. For example, the following text is difficult to understand and doesn

[gmx-users] Re: g_desort

Dear Jennifer: The line that worries me the most is: "I don't really want to try to figure out why gromacs-3.3.2 isn't working". First, I assume that you ran your mdrun under gmx-3.3.2 and I would think that you need to thoroughly understand why (and more importantly when) it broke. I may or

[gmx-users] Re: g_desort

Dear Jennifer: I have tried to download the package to reproduce your problem, but have been unable. http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Other_software links to G_DESORT.tgz, but that link sends me to: http://www.gromacs.org/@api/deki/files/54

[gmx-users] mix berger ff with opls

Dear Bin, I think that you are getting confused here between different publications. It was the Lindahl, E., and O. Edholm. 2000. paper that you quote below, but recall that they had no protein in that work so manipulations of fudgeQQ would have been available to them. The HEDP method is

[gmx-users] mix berger ff with opls

Dear Bin: Read the in-depth procedure here: http://www.pomeslab.com/files/lipidCombinationRules.pdf Note that the 0.125 scaling factor is not anything that you need to do in addition to the files that you can download from Tieleman's site -- it is already included there (you can confirm t

[gmx-users] Steered MD: Gromacs 4.0

Dear Matt: pull_vec1 = -31.07-15.37 9.89 is not equal to pull_vec1 = -31.07 -15.37 9.89 There could be other problems, but I would start there. -- original message -- Hi, I am having some trouble using the COM pulling code (Gromacs 4.0). I will try to describ

[gmx-users] Closing of .trr and .edr files after running out ofspace

Dear Sarah: From both of your posts, it appears as if you have corruption around this time (40 ns). Possibly your disk was temporarily full near that time. You could try to excise that portion with -b and -e combinations: trjconv -b 0 -e 4 -o a.trr trjconv -b 42000 -e 15 -o b.trr

[gmx-users] Closing of .trr and .edr files after running out of space

trjconv -e for the .trr eneconv -e for the .edr --original message -- Dear gmx-users, I have been very unfortunate (and stupid): I was running a simulation of 220 ns and due to limited space at our cluster-computer I was writing the .trr file and .edr file directly to another disc. That was

[gmx-users] rdf

Looks great to me... what's the problem? -- original message -- okay this should work http://docs.google.com/fileview?id=0B_QNmYARywUiNzE0MDA0NWMtYjFiMy00MTRjLThkNDMtNTk3NDgyNjcxZTgx&hl=en -Nisha Quoting chris.neale at utoronto.ca: I didn't get the attachment. Please upload the image to som

[gmx-users] rdf

I didn't get the attachment. Please upload the image to some website and post the link. --original message -- I saved my rdf plot as a pdf file and I have attached it to this email. Hopefully it will work. My system is one methane with 893 molecules of tip3p water in a cubic box of size 3

[gmx-users] mailing list search gives "Site settings could not be loaded"

I used http://www.gromacs.org/Support/Mailing_Lists/Search but it appears to be fine now... just a glitch I guess. On 1/31/10 10:25 PM, chris.neale at utoronto.ca wrote: Anybody else having trouble searching the gromacs archives? I get this message: Site settings could not be loaded We were u

[gmx-users] mailing list search gives "Site settings could not be loaded"

Anybody else having trouble searching the gromacs archives? I get this message: Site settings could not be loaded We were unable to locate the API to request site settings. Please see below for debugging information. HTTP Response Status Code: 0 -- gmx-users mailing listgmx-users@grom

[gmx-users] rdf

make a figure of your rdf, post it online somewhere (I use photobucket) and reply to the list with a link to your figure. Make sure your figure is well labeled and give us a thorough description of what you see that you don't like. Also tell us what your unit-cell box vectors are. Also desc

[gmx-users] error: Cannot compile and link MPI code with mpicc

Looks to me like you are not linking properly to the mpi libraries. Please post your gromacs compilation commands in full. For example, mine are posted below. Note also that some clusters make it more difficult for you depending on their setup. I have used clusters in which the simplest way

[gmx-users] Dihedral time of circulation

100 fs = 50 timesteps? I doubt it, but then again I have never checked and you're talking about a chi3 here, and one that involves a S with no hydrogens at that so I guess that it could occur quicker than I expected. However, you should avoid talking about "time for one rotation" without er

[gmx-users] Dihedral time of circulation

Dear Sa?a: There are many dihedral angles in the MET sidechain. I suspect that you mean to ask "how long does it take the chi1 dihedral angle of MET to equilibrate rotametric preference"? The answer is entirely dependent on context, with a free amino acid (perhaps also a methionine dipept

[gmx-users] Rotational PMF using angle_restraints_z and virtual definition

Hello, I am attempting to construct the free energy profile for rotation of a short peptide hairpin. For this purpose, I am using [ angle_restraints_z ]. I will focus this post on the simplified test system that I have been using to characterize the problem that I am experiencing: single

[gmx-users] density problems when switching from md to sd integrator

Dear Aymeric: 1. Can we please see the entire .mdp files for both simulations? I suggest that you use a tau_t=1.0 (0.2 is probably over-damped). 2. Although any value of tau_t should still produce the correct equilibria, your diffusion rates and your overall sampling may be slower with sd

[gmx-users] Restrict rotation between 2 molecules

Dear amir: You have 2 issues: 1. maintain planar plates 2. inhibit plate rotation. I think that the planarity is actually going to be a bigger problem for you (unless of course you want your plates to be able to bend). Position restraints in the relevant dimensions seems like a reasonable

[gmx-users] methane in water

Dear Nisha: I looked only at the rdf, and it seems entirely reasonable. 100 ns may be a long simulation, but you only have 1 methane and that's what leads to you having much less data than if you were for instance looking at water-water rdfs. If you want it to look smoother, then use larg

[gmx-users] simulation crash with GROMOS96 force field

Dear Vitaly: 1. No problem at all in vacuo? That with a 1 fs timestep and the sd integrator? Strange then that your molecule is ok and the water is ok, but they are unstable together. Perhaps your'e not getting any LJ interactions (or not correct ones) between your solute and water? That's wh

[gmx-users] CONSTRAINED SIMULATIONS

Dear Giuseppe: This is a pretty good example of how it can be useful to completely describe what you are doing at first posting. What you mention could easily be a problem for a couple of reasons: 1. The manual indicates that you may need more than one shake iteration in this case (or at

[gmx-users] simulation crash with GROMOS96 force field

All the directives are correct. Chris just mistyped saying [ molecules ] CIP 3 instead of [ moleculetype ] CIP 3 that I orginally send him. Not true. I meant exactly what I typed. I am referring to the section that occurs at the end of your .top file: It sometimes looks like this

[gmx-users] Re: simulation crash with GROMOS96 force field

Dear Vitaly: Justin raises the point well, so that should be addressed first. If, however, you still have problems then there's the only thing that I can think of: 1. put a single solute in a large vacuum box and use the sd integrator. Can you reproduce the problem? 2. Remove the dihedra

[gmx-users] CONSTRAINED SIMULATIONS

Dear Giuseppe: OK, those are the forces. They seem pretty huge and massively fluctuating, although I use umbrella sampling myself so this might be quite normal for constraint sampling (something for you to look into). The only thing that comes to mind is that your running up against a pbc

[gmx-users] Re: simulation crash with GROMOS96 force field

1. Is your system is properly minimized Of course, it is, based on the energy values. Don't be so sure! Although since your 0.25 fs timestep --> 1 fs timestep transition crashes you are likely correct here. **4. Why is there a 1-4 between atoms 62 and 80 if you have only water and a 42 at

[gmx-users] CONSTRAINED SIMULATIONS

Dear Giuseppe: *** What I am looking for is raw -pd pull.pdo data from the first run. *** It looks like you did not define a name for -pd: mpiexec -n $NSLOTS mdrun_mpi -np 1 -v -s start_res.tpr -o output_res -c output_conf -pi pull.ppa -pn mdgrp1.ndx -po pullout -pdo pullout1 * so based on

[gmx-users] CONSTRAINED SIMULATIONS

Dear Giuseppe: I don't think your method of showing the change is very good since it introduces unnecessary variables (e.g. did you use the correct files for the second run). What I am looking for is raw -pd pull.pdo data from the first run. I found no such file in the body of the email

[gmx-users] simulation crash with GROMOS96 force field

1. Is your system is properly minimized 2. If you take the output from a 500 ps run with 0.25 fs timestep and start a 1 fs timestep run, is that new run stable? 3. What are atoms 62 and 80? **4. Why is there a 1-4 between atoms 62 and 80 if you have only water and a 42 atom solute? 5. What do

[gmx-users] strange empty space inside the system box

Sounds like a bubble. Do some NpT equilibration by adding pressure coupling. That's going to be difficult with your freeze groups though. Basically, you need to find a way to get the correct solution density between the graphite layers. -- original message -- Hi all, Is there anyone who c

[gmx-users] CONSTRAINED SIMULATIONS

Please provide actual gromacs output and tell us where it is from. I know it's sad, but not all of us can recall what the gromacs 3.3.3 .pdo file format looked like. So please include a sufficiently large portion of the file to help us recall. If, on the other hand, these values that you pl

[gmx-users] fitting dihedral angle function parameters using gromacs

I have never done this myself. Nevertheless, I'm going to take a shot since you haven't got an answer yet. Dihedral parameters can be thought of as consistently developed fudge factors that are used to fine-tune a parameter set. The word consistent here implies that there is a method to dev

[gmx-users] Implicit Solvent

implicit solvent has apparently been implemented in the openMM modification of gromacs, although that is still in beta and is not to be trusted for production runs without doing your own testing. I have not tried it myself. You can obtain it here: https://simtk.org/home/openmm -- original

[gmx-users] COM Pulling

Try changing pull_dim = N N Y to pull_dim = Y Y Y And check the manual for what it does. Note that some of your other pull options are irrelevant tot he type of sampling that you appear to be doing, but that should not matter. Chris. -- original message -- I have a results of my MD and

[gmx-users] CHarmm and popc membrane

That's why I said if you know what you're doing :) ok, fair enough. The name flag is listed as [no]chargegrp I still don't see it (see below), is this [no]chargegrp new in the cvs ? I'm pretty sure that you're not referring to [no]lys, etc. $ /scratch/cneale/GPC/exe/intel/gromacs-4.0.7/ex

[gmx-users] CHarmm and popc membrane (response to "Missing Residues are list ind pdb file")

Hi Stefan and Pär, I believe that the latest response had the wrong subject, so I am changing it back. Pär, two comments: First, does that option really exist? $ /scratch/cneale/GPC/exe/intel/gromacs-4.0.7/exec/bin/pdb2gmx -h > z 2>&1; cat z|grep nochargegrp|wc -l Second, I am not entir

[gmx-users] The size of the domain decomposition grid (1) does not match the number of nodes (8).

Hello, I have a run that was working fine under parallel mdrun -pd and when I then switched to domain decomposition I got: Fatal error: The size of the domain decomposition grid (1) does not match the number of nodes (8). The total number of nodes is 8 while running like this: /scinet/gp

[gmx-users] Scaling of Coordinates is Occurring - why?

From what I can find, it seems that you are correct to assume that frozen coordinates should not be scaled: http://lists.gromacs.org/pipermail/gmx-users/2002-July/002054.html and, from the online manual: freezegrps: Groups that are to be frozen (i.e. their X, Y, and/or Z position will

[gmx-users] CHarmm and popc membrane

I think the notes from grompp are pretty clear. You need to redivide your charge groups so that they contain fewer atoms. You can do this in the .top or .itp file and you can find out how to do that in the manual. Feel free to post your original and charge-group-modified topologies back her

[gmx-users] Ammonia in Water

First, I doubt that you want a molecule with a partial charge. Second, just because the bonds, angles, and LJ parameters will be generated doesn't mean they will be correct. What are the N-H bond lengths of ammonia? Are those the same as the ones that you are including here? Take a look at

[gmx-users] SImulation error grompp

Probably you removed lipids from the gro but not from the top (which you need to do as well). Find a lipid atom name that occurs only once per molecule (In non-united atom lipids I use P8) grep P8 my.gro |wc -l This will tell you how many lipids should appear in your top file. Chris. --

[gmx-users] Error while pulling a settled tip4p water molecule

I have done a similar thing in the past (without using the pull code), renaming the crystal waters around the protein so that they were easier to track. I eventually figured out that it was necessary for me to place the waters sequentially in the .top file. e.g: ; This is OK Protein 1 SOL

[gmx-users] InflateGRO and trimer simulation

Try the doughnut mode in the newest version of the program -- it's meant for exactly this situation. http://www.csb.bit.uni-bonn.de/inflategro.html -- original message -- Hello Gromacs Users, I would like to run a simulation of a trimer in a DPPC membrane. I really like the elegant solution

[gmx-users] confout.gro contains PBC-broken molecules after EM in parallel with domain decomposition

Good idea Justin. I have posted as bug 386. -- original message -- On 1/9/10 1:44 PM, chris.neale at utoronto.ca wrote: Hi Justin, I can confirm that I see that code snippet in my md.c code, although my tests indicate that this is not the end of the story. I have now taken the output .gro, ra

[gmx-users] particle decomposition requires preliminary trjconv -pbc mol input

Thanks Berk, increasing -rdd from 1.0 to 2.5 has solved my problem. Note that the actual distance between the two atoms in the angle restraint never exceeds 0.9 nm, although this is a rather complex set of virtual atoms based on the positions of other virtual atoms, each virtual atom in i

[gmx-users] confout.gro contains PBC-broken molecules after EM in parallel with domain decomposition

Hi Justin, I can confirm that I see that code snippet in my md.c code, although my tests indicate that this is not the end of the story. I have now taken the output .gro, ran it through trjconv -pbc mol and then ran mdrun again under a variety of conditions: 1. EM(steep) mdrun_mpi NP=8

[gmx-users] PR for CG lipid and CG protein

Hi Justin, I just double checked and certainly the confout.gro from my EM run in parallel with domain decomposition in mdrun is broken over periodic boundaries. I'm running gromacs-4.0.5 on a nehalem under openmpi. Here is my .mdp file gpc-f101n084-$ cat em_pos.mdp define=-DPOSRES_INDO con

[gmx-users] PR for CG lipid and CG protein

Dear Sunny, I replied a while ago, but it seems to have not made it to the list. When using inflategro with gromacs3, you can run cycles like this: 1. inflategro.pl 2. mdrun (EM) 3. goto 1 When running with gromacs4, however, you must run cycles like this: 1. inflategro.pl 2. mdrun (EM) 3.

[gmx-users] particle decomposition requires preliminary trjconv -pbc mol input

future users experiencing this problem can follow this thread at: http://bugzilla.gromacs.org/show_bug.cgi?id=383 -- original message -- Hi, Can you file a bugzilla and attach the tpr file? Thanks, Berk Date: Tue, 5 Jan 2010 10:49:46 -0500 From: chris.neale at utoronto.ca To: gmx-users at gr

[gmx-users] low concentration simulation ?

Mark already answered this: http://lists.gromacs.org/pipermail/gmx-users/2010-January/047825.html --original message -- HI I am simulating the protein + ligand + water molecules system. In the experimental work, the concentration of ligand is pretty low, say under 20 mM (avearge 18 ligands att

[gmx-users] Error during minimization

Hi Nisha, you say "And it runs minimization with bad contact errors", but I don't see any indication of that error message here. Is it perhaps that your EM exits early and then your MD throws an error? In any event, please post complete error information as output by gromacs. Chris. -- origi

[gmx-users] Incomplete frame,while running trjconv .....

Your disk was full and the .xtc file could not be completely written, therefore you have an incomplete frame. I think that you have answered your own question here. If I was you, I would trjconv -e to get the full trajectory minus the last incomplete frame for a good .xtc file. There are ot

[gmx-users] angle_restraints_z and -ddcheck

I have determined that the proper solution here is to use particle decomposition. -noddcheck simply delays the inevetable fatal LINCS error. Nevertheless, mdrun -pd requires that one maintains whole molecules in the starting conformation: http://lists.gromacs.org/pipermail/gmx-users/2010-Ja

[gmx-users] particle decomposition requires preliminary trjconv -pbc mol input

Thanks Berk, I actually did not have continuation = yes. I still use old-style .mdp options unconstrainted_start and gen_vel (see below), although these get replaced by grompp. Quoting grompp: "Replacing old mdp entry 'unconstrained_start' by 'continuation'" gpc-f101n084-$ grep continuation

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