[gmx-users] chcl3.itp Invalid order for directive atom types

Hi Mohana, please be more specific (what mail did you read? what exactly is your problem, .itp, .top, command, etc.) and please post to the mailing list. If you would like to draw my attention to your post, then you can send me a separate email notifying me that you have posted something

[gmx-users] solvent spatial distribution

I agree with Mark, your question is not well formed. Perhaps what you are interested in can be obtained in the following way. 1. run g_spatial and load the grid.cube file in to vmd. 2. select the "volume slice" representation with the x/y/or z view as you desire 3. Find a way to superimpose

[gmx-users] phi/psi

http://wiki.gromacs.org/index.php/Dihedral_Restraints Chris. -- original message -- Hi ! I am using the gromos 96 force field to simulate a protein. Is there an option that which I can turn on during a MD run that would constrain side chain motion to within the ramachandran phi/psi values? In i

[gmx-users] Re: Onw question about rlist rvdw rcoulomb and nstlist

For treatments that require a non-zero buffer length, like shift and switch, you do this by setting rlist larger than rcoulomb. Coulomb should be fine with PME + straight cutoff and the difference for LJ between nstlist=1 and nstlist=10 I expect will be negligible for a 2fs timestep. Note t

[gmx-users] steered MD

Dear users, I would like to carry out steered molecular dyanmics simulations on one of my protein dimer. I have a few questions to learn regarding this. 1. The mdrun program needs -pn index.ndx file The way I understand is, we need to create the index file with groups (say atom1 to which the sp

[gmx-users] steered MD

My mistake. I suggest 500 kJ/mol/nm^2, not 500 kcal... sorry. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't p

[gmx-users] g_mindist -pi gives segfault in 3.3.3 and 4.0.2 but not 3.3.1

Hello, For my systems, I have been unable to get g_mindist -pi to function unless I roll back to gmx 3.3.1. Would somebody please test their 4.0.2 (and perhaps 3.3.3) installations to see if the error is repeatable or perhaps is somehow related to my installation? Related output from 3.3.3 w

[gmx-users] how to identify the hydrophobic core residue to calcuate gyration

make_ndx -f my.gro << EOF r ALA VAL TRP ... q EOF -- original message -- Hello guys, neone have idea how to mark which are the hydrophobic residue to supply with make index command and have to calculate the gyration curve. regards, ___ gmx-users m

[gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance

I just checked similar simulations of mine and Berk's suggestion accounts for similar discrepancies that I notice on a quick evaluation where g_traj and g_dist fail to give me the same distance as I obtain from the pull pos.xvg file. As Berk suggests, once I first trjconv -center -pbc mol -ur c

[gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance

mass 1 B 1 BBBB 1 0.000 9.00 [ system ] ; name Three atoms [ molecules ] ; name number 2 BBBB 1 Chris Neale wrote: I just checked similar simulations of mine and Berk's suggestion accounts for similar discrepancies that I notice on a q

[gmx-users] decoupling charge while maintaining intramolecular potentials

Hello, I am a new user of the free energy code. I am somewhat confused regarding the method that should be applied to decouple the long range interactions of the solvent from the solute while still maintaining intramolecular long-range interactions for the solute. I was able to find some

[gmx-users] why the trajectory file is not output

Hello Yang, It was asked twice if you ran serial or parallel and I did not see an answer to that question. we have seen segmentation faults with 3.3.1 and openmpi when running complex systems in parallel for systems that ran fine in serial. It was certainly a head-scratcher as it did seem

[gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance

Hi Steve, Noting Berk's comment, I should clarify that my runs were completed using 4.0.2 and were run in parallel, so you may be seeing something different than the discrepancy that I noted from g_dist or g_traj. Did you try the post-mdrun processing and g_dist test that I suggested here: htt

[gmx-users] ligand-protein distance restraint

Mark's suggestion of a hybrid [molecule] section is a good one. Please note the need to then include disre=simple in your .mdp file. Mark has previously posted an enhancement request for a grompp warning if you forget disre=simple in the .mdp file response to some confusion that I previousl

[gmx-users] free_energy = yes & init_lambda = 0.00 does not yield identical energies to free_energy = no.

Hello, when applying the free energy code, I expected that the instantaneous energy of a given conformation when free_energy = yes & init_lambda = 0.00 would be identical to that when free_energy = no. However, I have found this not to be the case in zero-step mdrun. This is the same result t

[gmx-users] Re: decoupling charge while maintaining intramolecular potentials

Thank you Michael for the detailed reply, I have posted clarifications and additional questions or remarks inline below. Hi, Chris- I unfortunately can't be too much help, because my free energy calculations are done through a modified version of Gromacs 3.1.4, and I am currently working with

[gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance

Hi Steve, I also use the pull code and would be very interested to more fully understand the problem that you are experiencing. However, I don't generally modify any code myself, and therefore have no use for your private system. What I would be eager to receive is your POPC-buckyball sys

[gmx-users] decoupling charge while maintaining intramolecular potentials

Thanks Berk and Michael for all of your assistance, Chris. -- original message -- I guess that what you want to do is exactly what the decouple mdp options do. You probably don't need modify any topology files. If couple-intramol=no (default) than all intra-molecular interactions are not turn

[gmx-users] range of magnitude for force constant

I see two potential problems that might arise with very large force constants. 1. If you start far from equilibrium your system will most definitely crash. It appears that this is not going to be an issue for you here though. 2. The less mass in your groups and the higher the force constant

[gmx-users] free_energy = yes & init_lambda = 0.00 does not yield identical energies to free_energy = no.

Hi Berk, the difference remains when utilizing double precision: free energy code on with lambda=0.00: Coulomb (SR) = -3.23064e+05 free energy code off: Coulomb (SR) = -3.22653e+05 Here are the full double precision values: ; Free energy control stuff free_energy = no Energies

[gmx-users] free energy with TIP4P bug fixed

Berk, David, and other developers, I believe that all the relevant information has already been posted, but since I use TIP4P ubiquitously, I would like to get some clarification regarding simulations that may be affected. I currently understand that: 1. Utilization of TIP4P in the absenc

[gmx-users] free energy with TIP4P bug fixed

I have done some tests that, for a single system, empirically indicate that the coulomb(SR) discrepancy occurs only with use of the free energy code and only when tip4p is in the same energygrps as any part of the molecule which is perturbed, even if the common atoms are not perturbed thems

[gmx-users] free energy with TIP4P bug fixed

I just realized that my previous post was incorrect on its final test. The correct conclusion is: I have done some tests that, for a single system, empirically indicate that the coulomb(SR) discrepancy occurs only with use of the free energy code and only when tip4p is in the same energygrps as

[gmx-users] free energy with TIP4P bug fixed

Since I also use the pull code on these systems (while not using the free energy code), I tested that system and verified that, for my system, the tip4p-based Coulomb (SR) discrepancy does not appear to result when the pull code is used in gromacs 4.0.3. With pull code and using energygrps

[gmx-users] free energy with TIP4P bug fixed

on't need to repeat all the calcs, and would like to use a consistent version, and (b) I am not sure that 4.x does not introduce additional bugs that might affect my calcs. Thanks!David On Jan 29, 2009, at 4:21 AM, Berk Hess wrote:Hi, The Coulomb energy difference that Chris Neale observe

[gmx-users] is the tip4p MW velocity treated differently in gromacs 3 vs 4

Hello, Does anybody know if there is a reason why the .gro output velocities would be different for tip4p MW in a zero-step mdrun between gromacs 3 and gromacs 4 (3.3.1 and 3.3.3 are the same, and are different from 4.0.2 and 4.0.3, which are themselves the same). diff gmx4.0.3/feoff.gro gmx

[gmx-users] is the tip4p MW velocity treated differently in gromacs 3 vs 4

Thanks David, you are correct about initial step constraints. More information inline below, but my question has been resolved. >Chris Neale wrote: >> Hello, >> >> Does anybody know if there is a reason why the .gro output velocities >> would be different for ti

[gmx-users] is the tip4p MW velocity treated differently in gromacs 3 vs 4

. Therefore it seems to me that something other than initial constraints is leading to this difference. Chris. -- original message -- Thanks David, you are correct about initial step constraints. More information inline below, but my question has been resolved. >Chris Neale wrote: >&g

[gmx-users] is the tip4p MW velocity treated differently in gromacs 3 vs 4

Thanks Berk. I am only interested in these velocities because I am trying to figure out why I am getting some differing results recently (which I will post later). I don't really care about the velocities output in the .gro this way, my interest was only based on the fact that I thought thi

[gmx-users] micelle disaggregated in serial, but not parallel, runs using sd integrator

Hello, I have been experiencing problems with a detergent micelle falling apart. This micelle spontaneously aggregated in tip4p and was stable for >200 ns. I then took the .gro file from 100 ns after stable micelle formation and began some free energy calculations, during which the micell

[gmx-users] micelle disaggregated in serial, but not parallel, runs using sd integrator

Thank you Berk, I will loon into tau_t=1.0 (or at least not = 0.1). Thank you for the hint. These simulations run in 200 ps segments and utilize restarts via grompp -t -e like this: EXECUTING: /hpf/projects1/pomes/cneale/exe/gromacs-4.0.3/exec/bin/grompp -f /scratch/4772976.1.ompi-4-21.q

[gmx-users] micelle disaggregated in serial, but not parallel, runs using sd integrator

Thank you Berk, I will repeat my runs using the checkpoint file and report my findings back to this list. Thank you for this advice. Chris. -- original message -- Hi, In this manner you use the same random seed and thus noise for all parts. In most cases this will not lead to serious artifac

[gmx-users] Parallel running of mdrun

I get one line like the following for each core in an mpi job: 5723 ?RL 0:38 /work/cneale/exe/gromacs-4.0.2/exec/bin/mdrun_mpi -deffnm ./md5_running/s6117B2_md5 -cpt 600 5724 ?RL 0:39 /work/cneale/exe/gromacs-4.0.2/exec/bin/mdrun_mpi -deffnm ./md5_running/s6117B2_md5 -cpt

[gmx-users] micelle disaggregated in serial, but not parallel, runs using sd integrator

It appears as if you were correct Berk. I will report on the results of my 24h test tomorrow, but I also set up another system that used ld_seed=1993 and ran in 20 ps segments instead of the 200 ps segments that I was previously using. This system shows signs of disaggregation on the 200 ps time-

[gmx-users] heat exchanges

The integrations errors in the electrostatics have much more effect on the water than on the protein, because the water has higher charges and is far more mobile. No thermostat can correct for these errors, unless you use multiple groups. I realize that it is not exactly a "thermostat", but the

[gmx-users] micelle disaggregated in serial, but not parallel, runs using sd integrator

My 24h tests on 200ps segments are also consistent with Berk's solution. SD runs with ld_seed=1993 results in a disaggregated micelle while ld_seed=-1 results in the same stability that I have seen previously using the MD integrator. This is not a surprise at this point, but I am posting the res

[gmx-users] heat exchanges

Thank you Berk, I have checked my temperature and find that there is no difference while using tau_t=0.1 or 1.0 (~2 ns): tau_t=0.1: temp=303.36 +/- 1.90 tau_t=1.0: temp=303.31 +/- 1.98 While using only one temperature coupling group, how would I ensure that the temperature of water is the sa

[gmx-users] Free energy perturbation of Cu(I) binding

You might benefit from reading Mobley, Chodera, and Dill. J. Chem. Theory. Comput. 2007, 3, 1231-1235. This paper doesn't relate exactly to your question, though, unless you do something like David initially suggested here http://www.gromacs.org/pipermail/gmx-users/2009-February/039436.html

[gmx-users] position restraint dynamics

If you want to know how much time is required for this step (assuming that this step is even required) then that is system dependent and something that you would ideally test for yourself. For example, after N ps of position restrained dynamics, how does that affect the RMSD of the protein

[gmx-users] pull code, lambda, and soft core availability

Hello, I see from looking at the source code that the free-energy lambda dependence is now available to the pull code based on pull_kB1. However, this leads to serious problems converging near lambda=1 when pull_k1=large and pull_kB1=0 and in the absence of a restraint (with k=0) the pull

[gmx-users] pull code, lambda, and soft core availability

Thank you Matt, that is indeed the perfect paper. I'll post back here once I figure out exactly where the (1-lambda)^2 term would fit into the pull code US equation. Chris. This seems to be a good reference for soft-core interactions. BEUTLER et al. AVOIDING SINGULARITIES AND NUMERICAL INST

[gmx-users] pull code, lambda, and soft core availability

Upon further investigation, it appears that a soft core may help in this case. This is in spite of the fact that the problem is not a singularity, but that the dgdl term (dgdl=0.5*(Fc_B-Fc_A)*(r-r0)^2) gives very large values for Fc_A large enough to be significantly restraining and Fc_B =

[gmx-users] g_wham Error bars

In addition to the suggestions made by Nicolas, you might try the wham program created by Alan Grossfield: http://membrane.urmc.rochester.edu/Software/WHAM/WHAM.html which is capable of doing a 'bootstrap' analysis of the error. If you have the available computational resources, then I beli

[gmx-users] how to get a solvent density map using volumeslice in VMD

Hi Jinyao, your question is not very well defined. It is considerably easier for me if you tell me exactly what you tried to get this to work, which I imagine was more than simply running g_spacial once and selecting the volume_slice representation in vmd. That said, 1. Can you view it as

[gmx-users] g_spatial and vmd volume slice (was "chris")

Dear Jinyao, 1. Your usage of trjconv prior to g_spatial is incorrect. trjconv -s a.tpr -f a.xtc -o b.xtc -center tric -ur compact -pbc none Since you didn't center your atoms of interest, you will not get good results. 2. what happens when you run g_spatial? Do you get some strange notes or w

[gmx-users] Possible to stop mdrun changing file names when using checkpoint files?

One option is to avoid checkpoint files all together. I personally use a grompp/mdrun cycle of ~2h segments that was historically done in order to utilize the -sort -shuffle options to gromacs 3. I found it simpler to keep on doing the exact same thing in gromacs 4, even though I no longer

[gmx-users] g_spatial and vmd volume slice

Dear Jinyao, this is quickly becoming a vmd-mailing list question, but I'll give it one more set of replies. I would appreciate if you would coallate these into a single how-to and put it on the gromacs wiki once you have figured out how to do it. >Dear chris, > Thank you for you help. > I

[gmx-users] g_spatial and vmd volume slice

Dear Xavier, "I have played with this recently and could not find the way to set or change the colors on the volume slice." see my previous post about how to do this with black/white and gimp/photoshop "Moreover I found that the colors, although clearly showing the expected pattern for th

[gmx-users] anomalous free energy dgdl.xvg values every nstlist steps while using a twin-range cutoff

Hello, I believe that the free-energy code dgdl contribution from the twin-range cutoff is being calculated incorrectly in gromacs 4.0.3 (and probably other versions as well). Specifically, I notice that the dgdl values spike at nstlist intervals. This can be seen directly from my dgdl.xvg a

[gmx-users] making .psf file based on .gro or .pdb

Download charmm and run it to make your .psf. There are some examples on the charmm forum. If you have further problems, you would be better to post to the charmm forum: http://165.112.184.13/ubbthreads/ubbthreads.php?Cat= If you need to make a .psf and only have a .gro, then use "editconf -f a.

[gmx-users] NVT or NPT ?

short answer: volume equilibration and therefore density equilibration. Even people who do constant volume production simulations usually do an initial constant pressure simulation to get the density correct. better answer: find a good simulation textbook and give it a read. Allen and Til

[gmx-users] g_spatial and vmd volume slice

Dear XAvier, "I have played with this recently and could not find the way to set or change the colors on the volume slice." see my previous post about how to do this with black/white and gimp/ photoshop I did not find any mention of this in your previous post. But it is ok. Sorry for

[gmx-users] anomalous free energy dgdl.xvg values every nstlist steps while using a twin-range cutoff

Thanks Berk, 4.0.4 does show the expected behaviour for me with the twin-range cutoff. Since I obtained 4.0.4 prior to mentioning this issue, I gather that you gave the free energy code a good looking-over recently. I really appreciate it. I have seen only one previous paper that utilized a

[gmx-users] combination rules -- the part about the combination rules

For LJ interactions, use [ pairtypes ]. For Coulombics there is unfortunately no analogous solution. I am not clear about exactly what you want to do. What "parameters" are you interested in, or by this do you just mean LJ and Q? Chris. -- original message -- Hello, I was wondering ho

[gmx-users] pull_pbcatom appears global and could benifit from a sanity check during grompp

Hello, I am using the pull code (umbrella, distance) to restrain molecule M to a specified distance from group G in gromacs 4.0.4. I recently found that I needed to specify pull_pbcatom(G) and restarted my simulations using a rationally selected atom from that group. However, the distance

[gmx-users] analysis using Gromacs tools

You will require a .tpr file for many analysis tools. In some cases, you can get away with a .ndx file. Check g_thistool -h to see what is mandatory input. You can make a .ndx file if you have a .pdb using make_ndx -f my.pdb -o my.ndx and then select your groups. If you need a .tpr file, th

[gmx-users] obtaining gromacs for ubuntu (was Re: gmx-users Digest, Vol 58, Issue 125 (akalabya bissoyi))

Dear akalabya, First some general suggestions on using this mailing list: 1. Please pick a relevant title as your subject 2. Please don't include an entire digest in your post, it is irrelevant 3. Please take some more time to format your question. "plz help me" doesn't actually invoke a strong

[gmx-users] pull_pbcatom appears global and could benifit from a sanity check during grompp

Thank you Berk, I did not realize that one might want to use a pull_pbcatom that is not part of the pull_group. In that case it makes sense that it should remain a global atom index. My comment regarding being affected by reordering the topology was indeed poorly constructed. What I meant w

[gmx-users] MPI_Recv invalid count and system explodes for large but not small parallelization on power6 but not opterons

Hello, I am currently testing a large system on a power6 cluster. I have compiled gromacs 4.0.4 successfully, and it appears to be working fine for <64 "cores" (sic, see later). First, I notice that it runs at approximately 1/2 the speed that it obtains on some older opterons, which is un

[gmx-users] MPI_Recv invalid count and system explodes for large but not small parallelization on power6 but not opterons

Thanks Mark, your information is always useful. In this case, the page that you reference appears to be empty. All I see is "There is currently no text in this page, you can search for this page title in other pages or edit this page." Thanks also for your consideration of the massive sca

[gmx-users] MPI_Recv invalid count and system explodes for large but not small parallelization on power6 but not opterons

Thanks Roland, The system has 500,000 atoms. I use PME and a 0.9 nm cutoff for coulombic and a 1.4/0.9 nm twin range cutoff for LJ. The interconnect is infiniband between power6 nodes that each have 32 cores @ 4.2 GHz that are multithreaded so that I can put 64 "tasks" on each node. The

[gmx-users] MPI_Recv invalid count and system explodes for large but not small parallelization on power6 but not opterons

Thanks Mark, The original link had a period after it that I did not recognize. The link does in fact work. This is quite useful, I will try to get some speed advantage out of it. Thanks again, Chris. -- original message -- chris.neale at utoronto.ca wrote: Thanks Mark, your information

[gmx-users] MPI-based errors on the power6 at large parallelization

Hello, This is a more detailed description of a problem that I previously reported under the title "MPI_Recv invalid count and system explodes for large but not small parallelization on power6 but not opterons" http://www.gromacs.org/pipermail/gmx-users/2009-March/040158.html but focuses

[gmx-users] about force fields

Be aware that for n-alkanes longer than ~8 carbons, the standard OPLS parameters will fail horribly. You will need to modify dihedrals or 1-4 interactions as is mentioned in some of the papers below. William L. Jorgensen, Jeffry D. Madura, Carol J. Swenson, "Optimized intermolecular potenti

[gmx-users] where is the position of the partial charges?

Hi Lin, The position of the partial charge is at the center of the atom (the "atom" is really only a point on which the functions are centered). If you want to change the position of the partial charge then you need to create another atom to carry that charge. Something like this is done with Ti

[gmx-users] OXY not found

of the transmembrane solubility and diffusion rate profile of dioxygen in lipid bilayers." Biochemistry. 2006 Sep 5;45(35):10719-28. Although that paper utilized the values directly from Marrink and Berendsen. ## Add to ffX.atp: ; Added by Chris Neale March 16 2006 based on ; 1) Fisher and

[gmx-users] phi / psi values using g_chi

two questions relative to g_chi from the gmx-3.3.1 but gmx-4.0.2 uses similar code. 1) In the header of g_chi obtained using the -h option there is a "bug" that indicates that the phi/psi angles are not calculated as the usual C(-)-N-CA-C and N- CA-C-N(+) definitions but H-N-CA-C and N-CA-C-

[gmx-users] phi / psi values using g_chi

I was either using using 3.3 or 3.3.1, certainly not 3.1.4 or 3.2.1. It looks like the change was in 3.3.1, possibly by Erik: [tera:~]?diff gromacs-3.3/src/tools/gmx_chi.c gromacs-3.3.1/src/tools/gmx_chi.c 2c2 < * $Id: gmx_chi.c,v 1.3 2005/02/16 17:39:27 hess Exp $ --- * $Id: gmx_chi.c,v 1

[gmx-users] free energy coupling/decoupling equivalence

Hello, I have just read an interesting paper suggesting that the reference state in free energy decoupling/coupling simulations should be the one with larger entropy. Lu and Kofke "Accuracy of free-energy perturbation calculations in molecular simulation. I. Modeling" JCP V. 114, N. 17 pp. 7303-7

[gmx-users] gmx in GPU calculation

generally, try to reduce the problem to something simpler. Therefore try the *exact* same thing on a non-gpu run. That said, it seems pretty clear that you created a .tpr file with a higher version of grompp and then tried to run it with a lower version of mdrun... or something like that, b

[gmx-users] Pull code using two reaction coordinates??

Hi Rodney, This may be possible if your reference is absolute coordinates. In this case, just use pull group 1 and 2, with the reference group undefined. For more nuanced usage, the problem is that you are only allowed one reference group (and one type of pull code usage) in a given run. I p

[gmx-users] some peoblems about modeling...

Please don't double post. We saw the first one. 1. That is a question with a lot of options. Do you want a grid of proteins? then try genbox -cp empty_big.gro -cs one_protein.gro 2. What do you mean by remove pbc? Try trjconv -pbc mol -ur compact to get an "enforced" pbc, or starting from

[gmx-users] Alert for Open MPI bug v1.3.0 and v1.3.1

Hello gromacs users, Since Open MPI is commonly used with gromacs, I thought that I would cross post this important notification that I received via the Open MPI mailing list. ### Quoting: The Open MPI team has uncovered a serious bug in Open MPI v1.3.0 and v1.3.1: when running on OpenFabr

[gmx-users] Error with equilibration of DPPC membrane with protein

Try gromacs 3.1.4 make_hole version, downloadable from the user contributions page. This works well for me. Alternatively, just select a bunch of lipids to remove based on g_mindist and equilibrate -- 50ns is cheap nowadays. The only reason that inflategro might be a huge advantage is if yo

[gmx-users] PMF calculation using pull code (constraint force method): constrained atom seems to be moving

1: Did you "constrain" or "restrain" the distance? Providing your .mdp file would help us to figure this out. The terms are quite different on this list. 2: The atom "danced around the expected position" ... are you sure that it "danced" around x and z, not just Y? 3: If your distance is

[gmx-users] missing interactions for the LJ-decoupled molecule during free energy in parallel but not serial

Hello, I am doing free energy calculations with gromacs 4.0.4. For the system I am using, I have reliable runs without any crashes when running in serial. When I run in parallel, I get stochastic crashes, that always have the same form (see below). Note that the "missing interactions" always

[gmx-users] missing interactions for the LJ-decoupled molecule during free energy in parallel but not serial

Thanks Berk, this makes sense to me. You were correct that my starting structure is fully Q+LJ coupled and it is only in the structures where there is no Q and I then couple LJ to lambda that I get this problem (and the extension that you suspect). I can just increase rdd. I was actually us

[gmx-users] Pressure Coupling Problem

Hi Ilya, First thing that comes to mind is that it is strange to couple a coulombic switching function with PME. While this could possibly be done correctly, I doubt that it is in fact done in the way that you expect (i.e. correctly) in gromacs. In fact, I think that grompp/mdrun should p

[gmx-users] Pressure Coupling Problem

Hi Ilya, If you did include the entire mdp file then you have a time step of 4 fs and no constraints (other than water). For a timestep of 2 fs, you should constrain all-bonds (or some would say at least h-bonds) and for 4 fs then you should also constrain angles involving hydrogens (need

[gmx-users] Pressure Coupling Problem

You say "I run all he sims with constraints=all-bonds", but I don't see that in the mdp options that you provided. I even put your text in a file and grepped for it just to be sure. Did you only give us a partial mdp file? Try adding this to your mdp file: constraints = all-bonds

[gmx-users] Re: Membrane protein tutoria

Dear Pawan, I suggest that you try doing some protein in water simulations or some available tutorials before you proceed with your bilayer study. You might also consider reading the error messages more carefully and attempting to troubleshoot based on these messages. If the error message

[gmx-users] Pressure Coupling Problem

So your problem with the small water box was solved simply by adding more minimization? I then suspect that all of your problems are simply related to a bad starting structure -- and by the sound of it is really is very bad. Are you sure that you don't have an angstrom / nm problem here? Chris

[gmx-users] Pressure Coupling Problem

arlier. No matter how much minimization I do the volume of the box expands when run it using berendsen pressure coupling with a tau_p -f .1. Ilya On Thu, Apr 9, 2009 at 11:22 AM, Chris Neale wrote: [Hide Quoted Text] So your problem with the small water box was solved simply by adding more

[gmx-users] problem in insertion of protein into lipid bilayer in proper orientation

Use gromacs 3 for the editconf -princ step. -- original message -- Dear justin Thanks for tutorial on membrane protein simulation . I am following your tutorial, everything is fine but problem came in concatanation . After orrienting the protein by using editconf I did the

[gmx-users] Generating topology file for a molecule (FNP) not in the gromacs library.

When actually building the topology I find it easiest to create the residues in the relevant .rtp and allow pdb2gmx to build the topology for you. However, all this does is correctly connect everything and put your parameters where they should be. All previous comments (in this thread and the h

[gmx-users] Problems with GROMPP

I'd echo Justin's request for your *actual* commands. Computers are very literal, and we'd rather have your original commands than something that's clearly been filtered through your head. If the above reflects your actual use of wildcards on the command line, that sounds like a possible source of

[gmx-users] about parallel run

What i was trying to do is to run a parallel simulation. I have successfully compiled mdrun with mpi support. This is my grompp command grompp -f md.mdp -c rec_pr.gro -p rec.top -o rec.tpr -np 12 And this is the script I sent to the cluster: #!/bin/bash cd /home/yunierkis/MD export LAMRSH="ss

[gmx-users] Re: image control

Email them to me and I will post them on the internet and provide links to this list. chris.neale |at| utoronto.ca Hi Myunggi Yi, I said link them, not mail them to me. Check your .tpr file to see 1. whether these parts of your lipids are already separated at the start of the equilibration

[gmx-users] Parrinello-Rahman coupling and constant slight evolution of box sides

I note this from your .mdp file: rvdw = 1.4 I assume that you use the Berger lipids (I don't see POPE in ffG43a2.rtp). Since those were parameterized for rvdw=1.0 you may want to consider the effect of rvdw=1.4 as in appendix A in Patra, Karttunen, Hyvonen, Falck, Lindqvist,

[gmx-users] deshuf.ndx doesn't work for forces?

Message: 2 Date: Wed, 23 Jan 2008 18:56:22 -0500 From: LuLanyuan <[EMAIL PROTECTED]> Subject: [gmx-users] deshuf.ndx doesn't work for forces? To: Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="gb2312" Hello All, I found sth like a bug regarding the deshuffle index file. I di

[gmx-users] deshuf.ndx doesn't work for forces?

OK, I can confirm this for 3.3.1. However, I don't think that the problem is one of shuffling or sorting but simply that trjconv -f a.trr -o b.trr creates an exact copy of the .trr file *without* the forces. You can easily verify this by doing this: trjconv -f a.trr -o b.trr gmxdump -f a.trr >

[gmx-users] Re: deshuf.ndx doesn't work for forces?

My apologies, The commands should have been: trjconv -f a.trr -o b.trr gmxdump -f a.trr > a.dump gmxdump -f b.trr > b.dump diff a.dump b.dump > ab.diff Chris Neale wrote: OK, I can confirm this for 3.3.1. However, I don't think that the problem is one of shuffling or sorting b

[gmx-users] Re: deshuf.ndx doesn't work for forces?

/>/ From: chris.neale at utoronto.ca <http://www.gromacs.org/mailman/listinfo/gmx-users> />/ To: gmx-users at gromacs.org <http://www.gromacs.org/mailman/listinfo/gmx-users> />/ Subject: [gmx-users] Re: deshuf.ndx doesn't work for forces? />/=20 />/ My apologies, The

[gmx-users] grompp problem

/ Hello! />>>/ />>/ I've tried to prepare a file for the mdrun and when I use grompp I get the />>/> massage that there is a fatal error in grompp.c line or line 1109, />>/> respectively. / />What command are you issuing? What's in the .mdp file? What is the *exact* />>/error message? />

[gmx-users] Question about analysing micelle structure

I've been studying about the structure of a nanoemulsion of palm-oil and surfactant in water. Many simulations have been performed. My first objective is to replicate the experimental work done and then study the structural properties. I'm using GROMACS (its free, flexible, and fast!!). Simulatio

[gmx-users] dihedral restraints in v3.3 different than v3.3.1 (or broken)

This is just a notice for the archives. I was recently working on a new cluster where only gromacs 3.3 is installed. It took me a while to figure out that the [ dihedral_restraints ] section is either differently implemented or broken in 3.3 compared to 3.3.1. Since the online list of revis

[gmx-users] ihedral restraints in v3.3 different than dihedral restraints in v3.3 different than v3.3 (or broken)

I try to perform dihedral_restraints on protein helices. Searching on this subject in the gromacs manual, wiki.gromacs and gmx-mailing list give me some clue but it is not clear for me yet. Also I did some you suggest in following address: http://www.gromacs.org/pipermail/gmx-users/2006-D

[gmx-users] dihedral restraints wiki section

I have added a section on dihedral restraints to the wiki. http://wiki.gromacs.org/index.php/Dihedral_Restraints ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://w

[gmx-users] Problem regarding Complex ion addition by genbox

I tried with genbox option with perticular concentration i.e. perticular number of each component like guanidium ion thiocynate ion & water molecule.But while doing PR(position restrain MD) it showing errors : constraints errors in algorithm shake at step 0. t=o.oo ps : water molecule starting at

[gmx-users] Problem regarding Complex ion addition by genbox

Thanks for giving me insight. But i have a query. I tried to add complex ion by genion but while adding, it replaces the water molecule according to my choice but it shows information of one atom only not of all atom of that complex molecule in structure file (.gro).i then tried to use by genbox.H

<    1   2   3   4   5   6   7   8   9   10   >