[gmx-users] Re:problem with simulation of freezing of water

Hi, Also note that it is difficult to simulate the right structure of ice (Ih). You didn't write what you want to study, but search the literature carefully. You may need to use an ab-initio model. Ran Message: 7 Date: Sun, 11 Nov 2012 11:26:19 -0500 From: Justin Lemkul Subject: Re: [gmx-users]

[gmx-users] Re: genion problem with divalent ions

. Ran ---- Ran Friedman Biträdande Lektor (Assistant Professor) Linnaeus University School of Natural Sciences 391 82 Kalmar, Sweden Norrgård, room 328d http://lnu.se/ccbg On 9 September 2012 16:10, wrote: > > &

[gmx-users] RE: quasi-harmonic entropy calculation

Hi, IIRC I tested g_anaeig when David wrote it and the results were the same as calc_entropies.pl, so it sounds strange. Are you sure you use the same input in both cases? Did you use the eigenvectors that correspond to the same eigenvalues? Also, how may eigenvalues are close to zero? Ran Mess

[gmx-users] RE: g_clustsize

ou need it. g_clustsize doesn't give you the radius of gyration of the cluster. My modified version does, but only for the largest cluster - not for all as you need I guess. Good luck, Ran -------- Ran Friedman Biträdande Lektor (Assistant Profe

[gmx-users] RE: Including quadrupole-charge interaction in GROMACS (WU Yanbin)

and Meuwly, M", title = {Higher order multipole moments for molecular dynamics simulations}, journal = "J Mol Model", year = "2009", volume = "15", pages = "687-694" } Ran ---- Ran Friedman Biträdande Lekt

[gmx-users] Re: oplsaa vs. charmm (Thomas Evangelidis)

disease.}, journal = "Protein Sci", year = "2009", volume = "18", number = "4", pages = "792-800", month = "Apr", pmid = "19309732", url = "http://www.hubmed.org/display.cgi?uids=19309732";, doi = "10.1002/pro.87" }

[gmx-users] RE: Essential dynamics - concepts (Kavyashree M)

From: Tsjerk Wassenaar Subject: Re: [gmx-users] Essential dynamics - concepts To: Discussion list for GROMACS users Message-ID: Content-Type: text/plain; charset=ISO-8859-1 Hi Kavya, > Its g_covar contributed by Dr. Rossen apostolov if I am right.? Here it > states that those which are having

[gmx-users] RE: Metal surfaces (Sergio Manzetti)

aces}}, Journal = {JOURNAL OF PHYSICS-CONDENSED MATTER}, Year = {{2009}}, Volume = {{21}}, Article-Number = {{424108}} } Ran Friedman Biträdande Lektor (Assistant Professor) Linnaeus University School of Natural Sciences 391 82 Kalmar, Sweden No

[gmx-users] RE: micelles and trjconv -pbc cluste

users] Re: micelles and trjconv -pbc cluster To: gmx-users@gromacs.org Message-ID: <401162.89007...@web35301.mail.mud.yahoo.com> Content-Type: text/plain; charset="iso-8859-1" Dear Ran Friedman and Tsjerk Wassennaar, ? ?First of all, thanks to all responses to my problem. As far as t

[gmx-users] RE: micelles and trjconv -pbc cluster

Hi, Likewise, I have a modified version of g_clustsize that calculates the radius of gyration for the largest structure and can send you the code. Ran Ran Friedman Biträdande Lektor (Assistant Professor) Linnaeus University School of Natural

[gmx-users] RE: Regarding DCCM analysis with g_covar available in user contributed section

h Subject: Regarding DCCM analysis with g_covar available in user contributed section Hello, I am using g_covar vailable in user contributed section (by Ran Friedman) the description available for the package is as follows: "This package contains a modified version of g_covar, which can pri

[gmx-users] Re: RE: simulation of a metal binding sites (bharat gupta)

y of Zinc Containing Proteins and the Development of the Zinc {AMBER} Force Field ({ZAFF})}, journal = "J Chem Theory Comput", year = "2010", volume = "6", pages = "2935-2947" } You have to know quite a lot on the structure to use this approach. Good luck

[gmx-users] RE: simulation of a metal binding sites

Hi, There are methodological difficulties in simulating multivalent ions together with proteins. Check the mailing list for a discussion and reference. This is not an issue of Gromacs but of dealing with protein-ion interactions using a classical non-polarisable force field. Check the literatur

Re: [gmx-users] Simulation using Martini force field

er (on the protein FF) about the definition of secondary structure. Best regards, Ran -------- Ran Friedman Biträdande Lektor (Assistant Professor) Linnaeus University School of Natural Sciences 391 82 Kalmar, Sweden Norrgård, room 328d +46 480 446 290 Teleph

RE: [gmx-users] .psf and .dcd files

Hi, psfgen is a part of VMD but maybe you can also use it separately. Note that you have to give it the right input and parameters, and I don't know if it works with AMBER-FF. Good luck Ran From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.o

RE: [gmx-users] .psf and .dcd files

Hi, You can use wordom to convert .xtc files to .dcd. As for the .psf AFAIK you'll have to work on it yourself using CHARMM or psfgen. Ran ---- Ran Friedman Biträdande Lektor (Assistant Professor) Linnaeus University School of Natural Sciences 3

RE: [gmx-users] proton proton transfer

Sorry for the typo below. DFT based *or* semi empirical code. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Ran Friedman Sent: 02 December 2010 15:01 To: Discussion list for GROMACS users Subject: RE: [gmx-users] proton

RE: [gmx-users] proton proton transfer

ant to use QM/MM (implemented in Gromacs) or simulate your system with a DFT-based 'on semi-empricial code. Ran -------- Ran Friedman Biträdande Lektor (Assistant Professor) Linnaeus University School of Natural Sciences 391 82 Kalmar, Sweden Norr

RE: [gmx-users] Claculating Equilibrium constants

Phys Chem Chem Phys. 2009 Feb 14; 11(6): 975-83 Good luck, Ran Ran Friedman Biträdande Lektor (Assistant Professor) Linnaeus University School of Natural Sciences 391 82 Kalmar, Sweden +46 480 446 290 Telephone +46 76 207 8763 Mobile ran.fried

[gmx-users] RE: Gibbs free energy of binding

romacs and Wordom. All have their limitations, but the same is true for experimental measurements of entropy changes upon binding. Ran -------- Ran Friedman Biträdande Lektor (Assistant Professor) Linnaeus University School of Natural Sciences 391 82 Kalm

Re: [gmx-users] RE: Targeted MD

Hi, -r and -rb are for FEP. If you want to bias your simulation's sampling, you can use the pull code, essential dynamics sampling or flooding, all of which are described in the manual and literature. Ran Nimesh Jain wrote: > Hello, > > I realize that this topic has been discussed before, but I

Re: [gmx-users] Is there a way to calculate the hydrodynamic radius using GROMACS?

e at http://www.gromacs.org/search before > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- --

Re: [gmx-users] Entropy from NMA

roduced (still, with small size). Running g_nmeig in these > "parallel" mtx results in huge all-negative eigenvalues. > The same input in single-node goes just fine, with first 6 eigenvalues close > to zero. > > > Rui Rodrigues > > > > > On Wed, 28 Jul 201

Re: [gmx-users] Entropy from NMA

Hessian... > > > Writing Hessian... > > > Writing Hessian... > Finished step 1400 out of 1400 > > Writing Hessian... > > Back Off! I just backed up nmatpr.mtx to ./#nmatpr.mtx.2# > > It gives me negative eigenvalues. > > One would expect it sh

Re: [gmx-users] Entropy from NMA

p.s. How big is this negative value? Ran Friedman wrote: > Hi, > > Can you post the exact commands you used for EM and NMA? > > Ran > > nahren manuel wrote: >> Dear Gromacs Users, >> >> I am trying to calculate Entropy from Normal Mode An

Re: [gmx-users] Entropy from NMA

coulomb-switch= 1.0 > rvdw-switch= 1.0 > vdwtype = shift > rcoulomb = 1.3 > rvdw = 1.3 > > -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zu

Re: [gmx-users] NPH Simulations

this? > > Thank you > Sapna -- ---------- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Email: r.frie

Re: [gmx-users] g_cluster Jarvis-Patrick

Hi, The nearest neighbours are defined according to RMSD between the structures. If M=10, a new conformation x is added to a given cluster when a conformation y in the cluster exists such that: (1) x and y are neighbours, i.e., x has y among the 10 conformations with minimal RMSD to x and vice ver

Re: [gmx-users] Re: g_cluster settings

Marc - Note that you used the linkage method which maps a structure to a cluster if its distance to any structure already in the cluster is is less than the cutoff. If you think it's not representative of your system try another clustering method, but note that you may need a longer trajectory as w

Re: [gmx-users] large forces and monstrous water molecules in energy minimization step

-- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Email: r.fried...@bioc.uzh.ch Skype

Re: [gmx-users] Electric field, potential, dielectric constant

Hi, You may want to use a Poisson-Boltzmann solver, e.g., APBS for this purpose. Ran Vladimir Lankevich wrote: > Dear Gromacs Users, > > I have several questions about electrostatics in Gromacs. > I am simulating two proteins in water, separated by certain distance, > and was interested in their e

Re: [gmx-users] Re: Simulation with CsCl

x-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before > posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to

Re: [gmx-users] How to increase the tolerance for conjugate gradient minimization

Hi Arthur, The most useful option from my experience is to run Gromacs in double precision. You also can try to make emstep smaller (after an initial minimisation of the crude structure) and use l-bfgs. Good luck, Ran -- -- Ran Friedman

Re: [gmx-users] g_cluster, RMSD distribution

Hi, The distribution is calculated as follows: 101 bins are formed between zero and maximum rmsd in equal separation (by calculating the largest value by 100 to create the separation). Each rmsd value is put into the right bin and the counter for that bin is increased by 1. The total number of cou

Re: [gmx-users] about SHAKE, SETTLE, LINCS and double x single precision

Hi Alan, I don't think using single precision is much of a problem when using thermostats, regardless of the constraint on the water. See also Berks' comments: http://oldwww.gromacs.org/pipermail/gmx-users/2010-March/049137.html http://oldwww.gromacs.org/pipermail/gmx-users/2010-March/049152.html

Re: [gmx-users] protein Aggregation using Gromacs

nce analysis tools, e.g., TANGO > http://tango.crg.es/ > > Good luck, > Ran > > -- > -- > Ran Friedman > Postdoctoral Fellow > Computational Structural Biology Group (A. Caflisch) > Department of Biochemis

Re: [gmx-users] protein Aggregation using Gromacs

than what one can simulate using atomistic MD. For a quick approach you can use sequence analysis tools, e.g., TANGO http://tango.crg.es/ Good luck, Ran -- ------ Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caf

Re: [gmx-users] Normal Mode Analysis

Hi, NMA is not MD - for one thing you don't run an NMA simulation for a certain time. I suggest you read about NMA and make sure you understand what the method does and what it can achieve before continuing. There is some data on the manual, a lot of data on the web and even more in books. When yo

Re: [gmx-users] Dynamics cross correlation map

h before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Ran Friedman Postdoctoral

Re: [gmx-users] Turn-off water optimisation

Hi, Can you also post your .mdp? Ran Berk Hess wrote: > Hi, > > I have never heard about problems like this before. > It seems highly unlikely to me that the innerloops are causing this. > > Are your running exacly the same tpr file on your local machine > and the cluster? > > You probably want

Re: [gmx-users] NVE of water

Berk Hess wrote: > > > > Date: Mon, 1 Mar 2010 15:44:28 +0100 > > From: r.fried...@bioc.uzh.ch > > To: gmx-users@gromacs.org > > Subject: Re: [gmx-users] NVE of water > > > > Mark Abraham wrote: > > > On 2/03/2010 12:39 AM, Ran Friedman wrote

Re: [gmx-users] NVE of water

Mark Abraham wrote: > On 2/03/2010 12:39 AM, Ran Friedman wrote: >> Hi, >> >> I would still argue that double precision is important. > > Oh? The discussion of Table 4 of > http://pubs.acs.org/doi/abs/10.1021/ct700301q (2008 GROMACS 4 JCTC > paper) suggested to m

Re: [gmx-users] NVE of water

art = yes >> > > constraints = all-bonds >> > > constraint_algorithm = shake >> > > shake_tol = 0.0001 >> > > ;VdW >> > > vdwtype = Switch >> > > rvdw = 1.0 ; rvdw+ (0.1:0.3)= rlist >> > > rvdw_switch = 0.9 >> > > gen_vel

Re: [gmx-users] NVE of water

= no > optimize_fft = yes > > Any suggesions are really welcome. > > Thank you. > > Regards, > Andrea Muntean -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Bio

Re: [gmx-users] Assembling a good simulation starting point

r your advice!   John Ladasky ------ Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Institute of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-

Re: [gmx-users] problem normal mode analysis

Hi, I guess posting the whole set of commands you used and mdp file for NMA can help. Best, Ran sarbani chattopadhyay wrote: > hi, > I want to do a normal mode analysis on a small peptide. > I had complied gromacs in double precision and energy minimized the > structure in vacuum, > using steepest

Re: [gmx-users] intrapeptide hbond existence map

Hi Stephane, The map shows weather a certain hydrogen bond exists at a certain time. In principle you can get the information by integrating this data, but I'm not sure it can be done without changing the code. A possible solution is to use a script and run g_hbond -num 28 times with two relevant

Re: [gmx-users] Problem with OPLS Benzene and Bond Constraints

Dear Mike, It's hard to know what's going on from your input. Did you check the thermodynamic components with g_energy (especially the pressure bond, LJ and Coulomb energies)? This may give you a hint. Also, I would do a test run with PME - you're anyway not following the parametrisation of Jorgen

gmx-users@gromacs.org

> fairuz zulkifli wrote: >> Hello everybody, >> I'm Fairuz from Malaysia. >> I just want to ask if there is someone that have information about >> PDB of ice and itp file of ice. >> I only had PDB of the ice and trying to convert it into itp file >> using GAMESS software. > > You can't. A .pdb fi

Re: [gmx-users] Re: Locally Enhanced Sampling with Gromacs

Hi, LES as developed by Elber is available in CHARMM and MOIL. Ran. Massimiliano Bonomi wrote: > Hi! > You may want to try PLUMED, which is the evolution of grometa > > http://merlino.mi.infn.it/~plumed/PLUMED/Home.html > > and can do also steered MD and umbrella sampling. > > Massimiliano > > On

Re: [gmx-users] Problems with g_hbond

Hi Rolf, Try renaming the atom names to something that starts with O and H for oxygen and hydrogen. Good luck, Ran. Rolf Erwin Isele-Holder wrote: > Dear users, > > I'm running a simulation which uses ethanol as solvent. When using g_hbond > the programm is able to recognize the solute's donors a

Re: [gmx-users] g_mindist -or inconsistencies with atom-pairs

Dear Shay, What do you get when -or is present? Do the atoms always belong to the same residues? I suspect that since the calculation of the minimal distance is made for all residues, what you get at the end is the atoms at minimal distance between the last two residues. This seems like a bug and

Re: [gmx-users] reference for make_edi -linacc

Hi Chris, Maybe in this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1303567/ Daidone et al., Molecular Dynamics Simulation of Protein Folding by Essential Dynamics Sampling: Folding Landscape of Horse Heart Cytochrome c Ran. chris.ne...@utoronto.ca wrote: > Hello, > > does anybody have a

Re: [gmx-users] using trjconv to get a 2x2x2 unit cell for traj.xtc

Dear Jenny, You can do this directly in VMD, using the Periodic tab under Graphics->Representations. Ran Jennifer Williams wrote: > > > Hello, > > I am trying to find a way around a visualisation problem I am having > in VMD. Some of my molecules go over periodic boundary conditions > meaning th

Re: [gmx-users] LIE method

. -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Email: r.fried...@bioc.unizh.ch Skype

Re: [gmx-users] Hydrogen bond occupancy for the dimer of Acetic Acid

o do measurement of distance between > molecules when they are bonded as a dimer... > > Best regards > Rasmus > > > Ran Friedman wrote: >> Hi Rasmus, >> >> A simple solution would be to run g_hbond twice, with two separate >> groups for acetate 1 as do

Re: [gmx-users] Hydrogen bond occupancy for the dimer of Acetic Acid

Hi Rasmus, A simple solution would be to run g_hbond twice, with two separate groups for acetate 1 as donor and acetate 2 as acceptor or vice versa, check the existence an hydrogen bond with g_hbond -num and write a script to check when the two hydrogen bonds co-exist. Hope that helps, Ran. Rasm

Re: [gmx-users] Constraints & Restraints

;>>> understanding is that "constraints" fix the position of an atom in >>>>> space and "restraints" restrain the deviation of the atom's position >>>>> from its equilibrium point. Is that correct? If so, then I am a >>>>&g

Re: [gmx-users] Docking with PyMol and using Gromacs

With VMD it's even simpler: use "dynamic bonds". Ran. Nicolas Sapay wrote: > > > Dallas B. Warren a écrit : >> >> Coordinate files like pdb and gro aren’t used by GROMACS to provide >> any bonding information. That is what the topology files are for. So >> their “presence” in your pdb isn’t an is

Re: [gmx-users] Martini simulation problem in recentering trajectory so that the bilayer is at the center

For quite a long time I had the feeling that trjconv doesn't resolve all situations. Following the very recent discussion between Roland Schutz and Tsjerk, I'm not sure there is an immediate solution. Ad hoc approaches such as preparation of tpr files from intermediate snapshots were useful for me

Re: [gmx-users] Is anyone also using lammps?s

or days. If I will not use PME, do I still need a fftw? > > -Peng > > On Wed, 4 Nov 2009, Ran Friedman wrote: > >> Hi Peng, >> >> It would be slower - never made any benchmarks on how much slower. But >> you don't run a very long simulation, do you? >

Re: [gmx-users] Is anyone also using lammps?s

Hi Peng, It would be slower - never made any benchmarks on how much slower. But you don't run a very long simulation, do you? Installing it isn't a problem. If you use PME you also need fftw in double precision though. Ran Peng Yi wrote: > > Hi, Ran, > > No, I haven't. I still have to find out

Re: [gmx-users] Is anyone also using lammps?s

Dear Peng, Did you also try to run GMX in double precision at some point? Ran Peng Yi wrote: > > I turned off the torsion interaction. The difference between Lammps > and Gromacs at integration time step 2fs was reduced. Details below: > > A melt of 240 n-octane (united-atom model), NVT, T=300

Re: [gmx-users] Is anyone also using lammps?s

nd a set of tau_t and tau_p? > I did mention the fluctuation, 100 kJ/mol for energy and 1 nm^3 for > volume. And I ran GMX in single. Not sure about Lammps, should be > double. All measured physical quantities converged well. Would you > expect differece if I compile GMX in double? Wou

Re: [gmx-users] Is anyone also using lammps?s

Hi Peng, Note that you're not using any bond constraints in Gromacs and a timestep of 2fs may be too long. Also, tau_t=0.02 seems too short for me. With 1fs timescale the agreement seem good enough, but you didn't include estimated errors so it's hard to tell. Also, I assume you run GMX in single

Re: [gmx-users] % of existence of hydrogen bond

Hi, You can use g_hbond -num and write a small script to calculate the percentage of h-bond existence per frame by calculating the number of frames for which a h-bond exists. Good luck, Ran. Moutusi Manna wrote: > > Dear all, > > I am dealing with a POPC+PEPTDE+WATER system. Basic residues

Re: [gmx-users] Advantage of NPT over NVT?

choose NPT. Parameters that deal with a thermostat and barostat are not straightforward to choose - there have been a lot of posts on this list about it. Even NVT is not simple. Ran. -- -- Ran Friedman Postdoctoral Fellow Computational Structural

Re: [gmx-users] g_hbond and fluor

David van der Spoel wrote: > Alvaro Cortes wrote: >> Hi all. >> >> I'm new at the list so i don't know if something similar has been >> discussed before. >> I tried to search in the archives, but i can't find something similar. >> >> I have a doubt about g_hbond and fluor acceptors. As i can see in

Re: [gmx-users] scalar correlation matrix

Hi, Check out the modified g_covar version with correlations, which is on the user contributions. Ran. sheerychen wrote: > Hello, everyone, > > Do anybody knows how to calculate the scalar correlation > matrix across the alpha carbon atoms, where the correlation function > is defined as: C

Re: [gmx-users] copper cluster bond to histidines

work. Think about that I > need to put a O2 molecule inside of the Cu2+ cluster in a second study. > > Any suggestion, comments and anything else are very welcome. > > Thanks in advance > > Regards > > andrea > > -- -

Re: [gmx-users] Switch - Shift function electrostatics

David van der Spoel wrote: > Emanuel Peter wrote: >> Dear Gromacs-users, >> >> At the moment I have a question which regards the different >> electrostatic algorithms mentioned in the Gromacs-manual. >> >> I did some simulations and I tried three different electrostatic >> algorithms: Cut-off, Shif

Re: [gmx-users] Re: Some questions on Tabulated Dihedral Potential

wrote: > Hi Ran, > > are you sure the derivative is calculated as: > der = (y[N+1] - y[N-1]) * 0.5 * deltaX > > and not as: > der = (y[N+1] - y[N-1]) * 0.5 / deltaX ? > > The last calculation makes a little more sense to me... > > -Johannes > > >>> Ran Frie

Re: 回复： 回复： [gmx-users] Re: So me questions on Tabulated Dihedral Potential

7;(x)? > CH > > > > > > -------- > *发件人：* Ran Friedman > *收件人：* Discussion list for GROMACS users > *已发送：* 2009/7/21(周二), 上午9:41:42 > *主题：* Re: 回复： [gmx-users] Re: Some questions on Tabulated > Dihedral Potential > > Ran Friedman wrote: >> Hi, >> &g

Re: 回复： [gmx-users] Re: Some questio ns on Tabulated Dihedral Potential

Ran Friedman wrote: > Hi, > > The numerical derivative for the Nth value y[N] is calculated as: > der = y[N+1] - y[N-1] * 0.5 * deltaX Correction: der = (y[N+1] - y[N-1]) * 0.5 * deltaX > where y is the potential deltaX is the difference between two > successive values in your

Re: 回复： [gmx-users] Re: Some questio ns on Tabulated Dihedral Potential

Hi, The numerical derivative for the Nth value y[N] is calculated as: der = y[N+1] - y[N-1] * 0.5 * deltaX where y is the potential deltaX is the difference between two successive values in your input (e.g., 1 if you have a table that goes from -180 to 180 with 361 values). I don't think you can

Re: [gmx-users] Re: Some questions on Tabulated Dihedral Potential

Hi, Johannes Kamp wrote: > Hi Cynthia, > > I'm also working on including some tabulated functions but I don't > have any simulation yet. Thus I'm not a 'specialist' in this topic, > but I hope I can help you a little. > >> Dear all, >> >> I tried to include 2 tabulated dihedral potential functio

Re: [gmx-users] indexing largest cluster with g_clustsize

before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- -- R

Re: [gmx-users] xdr library. Just for an example.

Hi Vitali, There should be such code with then library itself. Ran. Vitaly V. Chaban wrote: > Hi, > > Can anybody share any working code which uses xdr-1.1 library? - Just > to consult. > > Thank you very much in advance, > Vitaly ___ gmx-users mailin

Re: [gmx-users] lincs warning

Hi XAvier, Do you use virtual sites? I've seen this when I used virtual sites, large time steps and a system that probably wasn't equilibrated enough. Ran. XAvier Periole wrote: > > Dears, > > I am experiencing some problems running a few proteins in water > (GROMOS43a1/SPC) > with gmx-4.0.4 using

Re: [gmx-users] oplsaa parametrization

Hi Rosa, You can read the paper on PRODRG to study how they parametrise. There's a topology builder for OPLS-AA: http://labmm.iq.ufrj.br/mktop/ There're also commercial tools (see some previous posts on the mailing list) and you can also start with PRODRG and modify the files to have the right pa

Re: [gmx-users] oplsaa parametrization

R. A. wrote: > Dear Users > I m trying to simulate a structure (not a protein) which is not > parametrized in oplsaa FF. I created the structure using PRODRG and > included the results of *.itp from PRODRG to ffoplsaa.rtp file and > tried to use available oplss_xxx for my atom type near to those on

Re: [gmx-users] Re: MD with RMSD restraint

Hi, You can also use essential dynamics sampling. Ran. David van der Spoel wrote: > Sam Moors wrote: >> Hi, >> >> Position restraints do not allow me to do what I want. >> For instance, I want to allow the system to freely explore the >> conformational space within a certain RMSD range, but not ev

Re: [gmx-users] different result for entropy with normal mode analysis and schlitter-approximation

; > > > > ___ > 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 post (u

Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones

example: http://wiki.gromacs.org/index.php/Parameterization -Justin Regards, Josmar Rocha --- Em *sex, 27/3/09, Ran Friedman, Biochemisches Inst. //* escreveu: De: Ran Friedman, Biochemisches Inst. Assunto: Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigne

Re: [gmx-users] Re:Re: the vdw and electrostatic energy (Ran Friedman)

No. SR stands for short-range. Ran. > > I did not mean that. I want to know that when we use g_energy in > Gromacs to > read the energy from the file ener.edr, does the cutoff affect the values > of the energy? For example, when the cutoff is set to 1.2 nm and the PME > method > is

Re: [gmx-users] the vdw and electrostatic energy

nterface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemist

Re: [gmx-users] Topologies and charges for large organic ligands

Hi, The answer is (or should be) in: @article{Oostenbrink2004, Author = {Oostenbrink, C. and Villa, A. and Mark, A. E. and Van Gunsteren, W. F.}, Title = {A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6},

Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones

arameter sets are published in JCC, which may provide you with some useful information. -Justin > ------ > From: "Ran Friedman, Biochemisches Inst." > Sent: Friday, March 27, 2009 2:35 PM > To: ; "Discussion list for

Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones

Dear Josmar, You haven't written which force field you plan to use. For OPLS and AMBER QM-based optimisation should be fine. In Gromos, the FF was developed with the aim of reproducing experimental results and I'm not sure if you can find a better solution than examining other residues with th

[gmx-users] Re: g_covar

siest to compile the source code for various tools within GMX. It's not necessary, but it makes your life easier. Since your question doesn't refer to the modified g_covar code directly, I'm ccing the gromacs mailing list. Please keep future correspondence there. Good luck, Ran dar

Re: [gmx-users] Using R.E.D. charges with OPLS AA

ibe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- -- Ran Friedman Postdoctoral Fellow Computational Structural

Re: [gmx-users] gromacs 4 mpi weirdness

ting share/tutor/methanol/Makefile > config.status: creating share/tutor/speptide/Makefile > config.status: creating share/template/Makefile > config.status: creating share/top/Makefile > config.status: creating share/html/Makefile > config.status: creating share/html/images/Makefile > config.stat

Re: [gmx-users] initial velocities Langevin dynamics

___ > 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 post (un)subscribe requests to the list. Use the > www in

Re: [gmx-users] Conversion of trajectories to netcdf format

gromacs.org/search before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- -

Re: [gmx-users] gromacs 4.0.3 tests validations

Hi, I think the tests for pdb2gmx are outdated. Most fail due to warning(s) while running grompp, which were allowed with older versions. I'm not sure who maintains this tests - maybe a new version is due. Ran. Tru Huynh wrote: > Hi, > > I am compiling gromacs on CentOS-3 x86_64 both serial and LA

Re: [gmx-users] Barostat & Density decreasing to zero

Hi Omer, You use a dielectric constant is 80, which means that the electrostatic interactions are screened. Perhaps that's why your density is low. Ran. Omer Markovitch wrote: > Dear All, > I have simulated a protein inside a box with water and ions. I began > by minimizing my system (which has a

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

Berk Hess wrote: > Hi, > > That I have thought about and it would avoid a lot of trouble. > But I have not done that, because that would lead to different run results > every time you rerun grompp, which can be misleading when you are > trying to assess the effects of other parameters. > > But mayb

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

Hi, Maybe it's a good idea to have ld-seed=-1 as a default if that's not already the case. Ran. Berk Hess wrote: > Hi, > > I don't know why I did not add checks for ld-seed before. > Now grompp gives a note when continutation=yes and ld-seed!=-1. > > tpbconv will now generate a new ld-seed when re

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

Dear Berk, I think that g_clustsize has a similar problem. IIRC I fixed it in a similar way on my own copy. There are probably other tools that will suffer from this as well, but for g_clustsize it's important because it may deal with such groups. Same goes for trjconv, e.g., for a protein and li

Re: [gmx-users] g_clustsize

Vitaly Chaban wrote: > Hi Ran, > > I will try your advice. And for what purpose should '-mol' be used? > To cluster molecules. In this case, you topology is read from the .tpr file and all of the molecules there are taken into account for clustering. > Vitaly > > > RF> Hi, > RF> Use -n without -

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