[gmx-users] Multiple ppa files from a single parallel mdrun_mpi job

After taking a closer look at the code, I suspect that the problem can be resolved as follows. The call to: read_pullparams(pull, opt2fn("-pi",nfile,fnm), opt2fn("-po",nfile,fnm)); in pullinit.c should probably be protected by: if (MASTER(cr)) I have not tested this as it doesn't really matter

[gmx-users] Position restrain of protein and membrane

Thanks Justin for your reply, You mean to say that first keep PR on protein allowing the lipids to move(packing), later switch over to production run without keep PR on lipids? Here iam getting doubt that, While embedding protein into popc some of the lipids will be deleted led to creation o

[gmx-users] POPC number

I guess that depends on the size of your protein. You should have enough lipds such that the protein doesn't interact with its preriodic image. 90 POPC seem to be a bit to few for that. In my aquaporin simulations, I usually had something like 270 POPE molecules, but if you simulate a smaller prot

[gmx-users] optimizing the mailing list

I suggest that we consider ways in which the mailing list can be optimized. My initial thought is to allow submitters to flag messages as belonging to some particular topic(s). e.g. "program crash" "force fields" "protein" "free energy" "coarse graining" "lipids and detergents" "unknown" etc.

[gmx-users] Multiple ppa files from a single parallel mdrun_mpi job

Hello, I am running gromacs in parallel on a new system. I am also using the pull code. Everything appears to be going fine, except that I get backup copies of the .ppa files during a single call to mdrun_mpi. My best guess is that this is some type of mpi problem, but any pointers would

[gmx-users] Differences in version 3.0 and 3.3

Rgardng the Coul 1-4 interactions, are you only changing the executable in this comparison, or are you also (perhaps unintentionally) changing the .itp files? If so, could the difference be related to changes to the forcefield files as mentioned here: http://www.gromacs.org/pipermail/gmx-users

[gmx-users] G_SDF if reference atoms are in different residues

You could use g_spatial instead as that program requires you to do the reference calculation yourself with trjconv. I have not tried g_sdf in a while, but if you still would rather use that program, then you might be able to trjconv your own alignment and then somehow fool g_sdf into not do

[gmx-users] Vacuum Simulation Alanine Dipeptide =>minimisation: ERROR "No default Ryckaert-Bell. types"

>What do I have to adjust to get rid of the error message? did you try searching the archives? http://www.gromacs.org/pipermail/gmx-users/2006-September/023875.html http://www.gromacs.org/pipermail/gmx-users/2006-September/023872.html Chris. -- original message -- Hi, to create some toy data

[gmx-users] regarding 2002 post showing protein unfolding with long timesteps

David van der Spoel, can you please comment on this post of your from 2002: "long timesteps combined with dummies give me unfolding proteins while without dummies and 2 fs the systems are stable. These are long-time effects (i.e. after a couple of ns things start to happen). I have to do more tes

[gmx-users] FFTW & Gromacs installation on AIX 5.3

Hi Senthil, here is how I have compiled fftw and gromacs on an AIX. A warning though that the gromacs compilation usin the xlc_r compiler set took over 12h. First fftw: [EMAIL PROTECTED]:/hpf/data/pomes/cneale/exe/fftw-3.1.2_aix> cat cn_compile.sh #!/bin/bash export PATH=/usr/vac/bin:/usr/va

[gmx-users] charmm and oplsaa simulation results don't match

water is part of the ff, therefore see previous comments of Berk and myself. For a reference, see Ponder and Case 2003 (http://www.ncbi.nlm.nih.gov/pubmed/14631816), and while one of the pmfs that they present is quantitatively incorrect, the conclusions are valid: the different protein/water ff'

[gmx-users] charmm and oplsaa simulation results don't match

If a user could be assured that they would obtained the same microstates, even in an infinite simulation, then we could finally get rid of the multitude of ff's and pick 'one' since they would all agree. However, this is not the case. Therefore your assumption that you *should* get the same answe

[gmx-users] ensuring that compilation used gcc 3.x

Hey Chris When I downgraded to gcc 3.X I specified which compiler to use with CC= and CXX= then my log was 4.X-free. Have you tried that? I had not considered that. Thanks for the advice David, Chris. David Message: 3 Date: Mon, 11 Aug 2008 16:48:32 -0400 From: Chris Neale http

[gmx-users] ensuring that compilation used gcc 3.x

Hello, I am attempting to compile gromacs using gcc 3.x and I would like to confirm that I have actually obtained what I intended. In order to do this, I have set my path with the desired version of gcc first: export PATH=/tools/gcc/3.4.6/bin:$PATH However, I am not convinced that I am actua

[gmx-users] nature of gromacs / gcc-4.x problem

That sounds good, but I'm not sure if it is enough. Agreed. I'll recompile and start from previous checkpoints. Did you select "Closed bugs" as well? ouch! You're right, thanks for the tip. The error is mentioned here: http://bugzilla.gromacs.org/show_bug.cgi?id=108 and http://www.bionmr.com/

[gmx-users] nature of gromacs / gcc-4.x problem

Hello, I am trying to track down the exact nature of the gcc-4.1.x / gromacs bug. I have a system on which we were forced to reinstall gromacs (3.3.1 and 3.3.3) about 2 weeks ago and I didn't realize that the default gcc was bumped to 4.1.2. I am interested because ideally we won't need t

[gmx-users] membrane with OPLS force field

Sorry for my misunderstanding. You can not use standard OPLS parameters for lipids. Even if you go through the paramaterization process (see the gromace wiki and the original OPLS papers) then you are still stuck with the fact that standard acyl chain parameters fail when they get too long. I

[gmx-users] membrane with OPLS force field

ld find a membrane simulated with > the OPLS force field? I've never seen one either. The Berger parameters (commonly used) are based in part on OPLS parameters, and as such, Chris Neale has posted a nice procedure for modifying the Berger parameters (present at Tieleman's sit

[gmx-users] Fwd: membrane simulations with gromacs

ROTECTED] Reply-To: [EMAIL PROTECTED] Subject: membrane simulations with gromacs To: [EMAIL PROTECTED] Dear Chris Neale I'm a Ph.D student in computational chemistry and I try to simulate a GPCR in a membrane bilayer of POPC. Normally, I work with Amber package but Gromacs is mo

[gmx-users] Testing

I am reinstalling now - hopefully everything will work after that! Please do let this list know how it works out, either way, and even if you do submit a bugzilla (which would also be great). I am quite interested to know what you find. Chris. _

[gmx-users] Testing

This type of notification is a good idea, although I would suggest a few things. - Find a way to make this message visible to people who script their installation and redirect their output to log files. For example, if I get executable binaries and I can't find the word error or warning in

[gmx-users] Tyrosine problems again

Roll back to gcc 3.x. There is information available that says something like "don't use gcc 4.x, it is broken", but I stand by my previous comments that it is unfortunate that it is up to the end user to search the gromacs archives to find this out, not withstanding that it is a gcc-based

[gmx-users] Tyrosine problems again

Is there really no way to ensure that the compilation was 'successful' during the configure/make/make install procedure? While a compiler problem is technically not a gromacs problem in that it is not an error of the gromacs developers, I think that this is still something that deserves to

[gmx-users] DPPC bilayer

This should give you a good starting point for your own modifications. http://www.gromacs.org/pipermail/gmx-users/2006-September/023639.html http://www.pomeslab.com/files/lipidCombinationRules.pdf --original message -- Hello - I have previously asked about a DPPC bilayer and was very helpfully

[gmx-users] deprotonated cys

But of course then you also need to parameterize it, which is not a trivial task. OPLS does not have parameters for a cys thiolate; I'm not sure about other ff's. If you go back to the opls paper, you can follow the route by which they parameterized other ionized sc's. I have been considering d

[gmx-users] Possible Bug????

What do you get from gmxcheck -f eigenvec.trr ?? If you still have more problems you may want to consider submitting under a title that is a) more descriptive, and b) makes an attempt to avoid the word bug. --original message-- Users, I am having a problem when trying to convert a .trr to a

[gmx-users] Doubt regarding popc simulations

Unless your membrane is extraordinarily large, your cutoffs extraordinarily long, or your computational resources extraordinarily small, then I suggest that you simulate for 50ns and then analyze the convergence of these properties yourself. I have often posted the 50 ns suggestion to this list

[gmx-users] box size changing during isotropic pressure coupling

Here tau_p=4, which is already quite large. But there are no "real" problems in the system, the results should be fine. But the relative ling tau_p might be the reason for the strange scaling. This would make the scaling factor always close to 1 plus or minus one bit. I have not done the binary ma

[gmx-users] box size changing during isotropic pressure coupling

Thanks for the assistance Berk, Hmm... this is a (seemingly( really systematic decrease in x and y and increase in z. But is x at the start really EXACTLY identical to y? No. Here are the starting dimensions: 19.58000 19.39000 21.04200 That is prior to 200ps run with position restraints

[gmx-users] -pbc cluster with -center in trjconv 3.3.1

Hello, I have a DPC micelle in a rhombic dodecahedron. I want to use the pull code relative to the center of mass of the micelle and therefore I need to keep all detergent monomers in the same periodic image (otherwise I suspect that the COM will be calculated incorrectly). My problem is

[gmx-users] box size changing during isotropic pressure coupling

Hello, I have a system of 750,000 atoms consisting of detergent in water. Although this run has been carried out using isotropic pressure coupling, I see significant drift in the box dimensions over 150 ns. This run was carried out using gromacs version 3.3 and 3.3.1. I used the -shuffle and

[gmx-users] Question about Berendsen thermostat and Nose-Hoover temp coupling

Thanks David for sharing your knowledge, especially the note that for further information one can refer to the literature that was written around the time that these thermostats were released. I have a question though: by the way it is also true that if you use a thermostat or barostat th

[gmx-users] Question about Berendsen thermostat and Nose-Hoover temp coupling

Hi Justin, I wonder if you could expand upon the following statement, or perhaps offer some links or references. "Some argument can be made that N-H is more applicable to membrane simulations." I am interested because I use a Berendsen thermostat for membrane simulations. To be entirely

[gmx-users] box size changing during isotropic pressure coupling

A knowledgeable and helpful gromacs user has pointed me to some bugzilla comments: http://bugzilla.gromacs.org/show_bug.cgi?id=165 that reference revision comments: http://www.gromacs.org/gromacs/revisions/ Berk Hess 13 Feb 2008 box distortion with pressure coupling In all Gromacs versions

[gmx-users] Protein is moving out of box.

While the frequency with which this question is asked does of course say something about how diligently some users are searching the list archives and using the wiki before posting a question, it remains true that this is causing headaches for a significant number of new users. I therefore

[gmx-users] pull code yields non-zero separations at t=0

My appologies, I wasn't doing mass weighting to determine the initial offset. It works perfectly with a loop like this in g_com.c: clear_rvec(coms); coms_count=0.0; for(i=0; i^non-equilibrium simulations that will remove a ligand from a binding pocket in ^a directionally unbiased m

[gmx-users] pull code yields non-zero separations at t=0

Using gromacs 3.3.1: I am currently trying to using the pull code to do non-equilibrium simulations that will remove a ligand from a binding pocket in a directionally unbiased manner. As far as I can tell, some type of harmonic distance restraint is not possible using center of mass that has a mi

[gmx-users] berger-oplsaa combination for DPC micelle

ou should always post your relevant files with your question. It makes it easier for us to answer you. That said, I happen to have already used DPC and here is what I have done. I made a new dpc_rename.itp and it is quite different, but should simulate the exact same. Here is the beginning of the at

[gmx-users] berger-oplsaa combination for DPC micelle

the beginning of the atoms section ;Chris Neale modified atomtype names here to follow popc.itp ; Atoms double checked vs. popc.itp by CN Oct5 2006 [ atoms ] ; nrtype resnr residuatomcgnrcharge mass 1 LC3 1DPC C1 1 0.4

[gmx-users] Re: 1-4 scaling problem?

Dear Anindita, There is good reason to keep this on the mailing list. I am happy to help, but you are misrepresenting the situation to say that you received no answer on the mailing list. In fact, you received quite a bit of assistance: http://www.gromacs.org/pipermail/gmx-users/2008-May/034064

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

Interesting, I was not aware of that. For the simulations that I was discussing, we did not see that type of collapse on the 10ns timescale, although we started from extended structures and used very high temperatures since we were only interested in using MD as one of many methods to generate a

[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

[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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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

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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] non bonded interactions

Quoting: "The diameter of a C atom is about .3nm so I was surprised to see distances less than that." You mean the diameter (radius) as set in vdwradii.dat? This means nothing to mdrun, only special tools like genbox. energygrp_excl allows you to define: "Pairs of energy groups for which all

[gmx-users] Re: Total Energy protein only

Quoting Yoshiko Santoso <[EMAIL PROTECTED]>: Dear Chris Neale, Thank you very much for answering my questions in gmx-users mailing list. (See Below) > Hi gmx-users, Can anyone tell me how to find the total energy of the protein only (not the system)? You might try energygrp

[gmx-users] g_dist producing inconsistent values

I've since found the source of my problem - the program was measuring the (marginally shorter) distance across the PBC boundary, rather than the distance within the box. Unfortunately there doesn't seem to be a way to turn PBC images off (correct me if I'm wrong?), so I guess I'm going

[gmx-users] g_dist producing inconsistent values

I've since found the source of my problem - the program was measuring the (marginally shorter) distance across the PBC boundary, rather than the distance within the box. Unfortunately there doesn't seem to be a way to turn PBC images off (correct me if I'm wrong?), so I guess I'm going to

[gmx-users] grompp error "Not enough space" on IBM AIX

I have a large system of 0.7 million atoms. This system runs fine on opterons with 4GB of ram. However, grompp gives me an error that it has run out of memory on a new IBM AIX system that we have with 46GB of ram. Smaller systems work fine on both processors. In both cases I am running on 4 pro

[gmx-users] Total energy of protein only

Hi gmx-users, Can anyone tell me how to find the total energy of the protein only (not the system)? You might try energygrp_excl SOL SOL or energygrp_excl SOL SOL SOL PROTEIN depending on what you want to acheive. THis will take care of all of the nonbonded interactions. Without knowing wha

[gmx-users] Re: WARNING concerning lipid.itp

And again I will support myself :-) If you want to get more replies, you should include some more detailed information and also search the archives first (e.g. you might have found this: http://www.gromacs.org/pipermail/gmx-users/2002-July/001986.html by searching Overriding LJ-14 para

[gmx-users] analysis of POPC

There are fewer data for POPC than for DOPC and DPPC. If your force fields and methods give you good results for DOPC and DPPC, you should be in good shape for POPC, since the building blocks are the same, but just rearranged. Agreed. I add my emphasis to the given reference to the DOPC/DP

[gmx-users] Weird structure after minimization (membrane protein simulation)

Dear Mark and Chris, Thanks a lot for your suggestions which gave me idea to solve the problem. I have run the minimization again, without the FLEXIBLE water molecules. After the minimization, structure looks perfectly ok to me. please have a look at the new snapshoot. http://i269.photobucket.co

[gmx-users] NOE restraints and undefined hydrogen atoms, virtual interaction sites

There's no a priori reason why a mixture of a united-atom detergent sodium dodecyl sulfate and an all-atom peptide *couldn't* work. Neither is there any reason to suppose they *would* work without evidence that the SDS parameters were developed with this purpose in mind and suitably validat

[gmx-users] does grompp utilize forces from .trr files

Does anybody know if grompp uses the forces from a loaded .trr file in order to create the .tpr file? My interest is based on the fact that trjconv does not appear to deshuffle forces as it does for coordinates and velocities as presented in a recent gromacs thread starting here: http://w

[gmx-users] Weird structure after minimization (membrane protein simulation)

Thanks for your help. I have also tried the "comm_grps = System" option, and did energy minimization but after that also water molecular looked like the previous case (Figure-B, in my previous post). Thanks for trying that, I guess it was not the problem. As you mentioned on another post, 2.5A

[gmx-users] dihedral restraints wiki section

Ofcourse I'm worth your and others time since I reffered to some text and gromacs manuals as you and xavier suggest to me and I'm very appreciated. But I didn't give any clue. After all I try to be more precise about the replies. The best way to return the favour is to post a message back to the

[gmx-users] chloroform - oplsaa

The error message already tells you what is going wrong: Invalid order for directive atomtypes, file ""/usr/local/gromacs/share/gromacs/top/chcl3.itp"", line 1 so what is the first line from /usr/local/gromacs/share/gromacs/top/chcl3.itp ? It's [ atomtypes ] This is a parameter definition and sh

[gmx-users] Checkpointing GROMACS jobs

Steven Kirk wrote: / Hello, />/ />/ I have been using GROMACS for some very long (in wall clock terms) />/ simulations, and am curious as to how other users on this list solve the />/ problem of checkpointing long MD runs. It's a problem because of the />/ tendency of computational nodes in l

[gmx-users] Weird structure after minimization (membrane protein simulation

>Dear All, > >I am doing the simulation of POPE lipid + Protein, I did my system setup using mdrun_hole program. It looks fine to me http://i269.photobucket.com/albums/jj58/gromacs/all-three_final.gif (Figure-A). When I was doing energy minimization (using steepest decent and conjugant gradie

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

Thanks a lotfor responding me.Sorry for complexity. As you have suggest that in step 2. (2. Use editconf to put your guanidinium ion in a box of such a size so)> In input X.gro file in editconf there will be one guanidium ion or total number of guanidium ion that is required for desired concentr

[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

[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] 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] 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 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] Gel Phase in DMPC using Berger force field ?? -- Focus: naming convention

Several points: What is called the Berger force field was actually developed by See-Wing Chiu in our lab and presented in a 1995 paper. The Berger et al paper tested this force field against another candidate and found that it was better, and that is the paper that has been cited ever since. I

[gmx-users] different results when using different number cpus

Message: 4 Date: Wed, 05 Dec 2007 14:19:28 +0100 From: "Berk Hess" <[EMAIL PROTECTED]> Subject: Re: [gmx-users] different results when using different number cpus To: gmx-users@gromacs.org Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; format=flowed Hi, With Gromacs and (nearl

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