[gmx-users] Problems with solvation in SW (water shell model)

Hello, I'm trying to solvate an OPLSAA methanol molecule in polarizable water shell. Initially I generated a box of pure water using the TIP5P box available in gromacs 4.5. I simulated pure water and I got all the bulk properties in agreement with published results for SW water. In sequence, I

[gmx-users] Charmm foce field and free energy

Dear all, I'm trying to reproduce the hydration free energy of the methanol using the CHARMM force field. However I am getting a value considerably lower than the experimental: 17 kJ mol-1 (the experimental value is 21 kJ mol-1). Am I forgetting some technicality related to the force field? I

[gmx-users] Distance of pull group is larger than half the box size

Hello guys, I have tried to calculate the PMF for a dimer in a rectangular box of dimensions 3 x 3 x 7. However, the simulation stops when the COM separation is above 1.49 (ie half of the smallest dimension of the box. Since I am pulling along the Z axis at a distance that would be up to 3.5 nm.

[gmx-users] Silly little question about PMF - g_wham

Hi gmx-users, How do I plot the repulsive part of the PMF between two molecules that are approaching? I have achieved very good curves, but the potential never exceeds the coordinate reaction axis, stopping exactly at 0. Bests eef ___ Eudes Eterno Fileti

[gmx-users] Re: Pull code: separating molecules. distance and direction (SOLVED)

April 2012 10:28, Eudes Fileti fil...@gmail.com wrote: Hello everybody, I have used pull code to separate two molecules in water. The idea is to generate initial configurations for umbrella sampling. Initially I tried to use pull_geometry=distance. I noticed that the vector connecting the two

[gmx-users] Pull code: separating molecules. distance and direction

Hello everybody, I have used pull code to separate two molecules in water. The idea is to generate initial configurations for umbrella sampling. Initially I tried to use pull_geometry=distance. I noticed that the vector connecting the two molecules are not remained on the main axis of the box (z).

[gmx-users] Re: Isovalue for g_spatial representation

Dear Chris, thank you for information, they were very enlightening. Just one more question. Suppose I use an isovalue, say 10, I can say that the drawn surface is 10 times the average number density of solvent molecules? I am using -div option. Bests eef ___

[gmx-users] Isovalue for g_spatial representation

Hello gmx-users. I calculated the spatial distribution functions for my solvent-solute system. However I am in doubt in relation to the isovalue to be used in VMD to control the representation of the surface. The isovalue is admensional number or has some unit? There is some special criterium to

[gmx-users] g_velacc problem

Hi Florian, in fact I had already realized that it was possible to calculate the VACF without using the -m option (although this option was important for my calculations). I have not received any attachment, have you send me something? If necessary, please, send it to my email. Following your

[gmx-users] Re: g_velacc problem (Florian Dommert)

Dear Florian, thanks for the help. I wonder just one more thing. Is it possible to obtain the lateral diffusion coefficient in a specific plane (say xy) using g_velacc? Or it is only possible with g_msd? Bests eef ___ Eudes Eterno Fileti Física da Matéria

[gmx-users] Re: Re: Re: g_velacc problem (Florian Dommert)

...@icp.uni-stuttgart.de Content-Type: text/plain; charset=ISO-8859-1 -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 10/14/2010 04:41 PM, Eudes Fileti wrote: Dear Florian, thanks for the help. I wonder just one more thing. Is it possible to obtain the lateral diffusion coefficient in a specific

[gmx-users] Re: Re: g_velacc problem (Florian Dommert)

? ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 http://fileti.ufabc.edu.br On 10/12/2010 11:12 PM, Eudes Fileti wrote: Hi everybody, I'm trying to use g_velacc

[gmx-users] g_velacc problem

Hi everybody, I'm trying to use g_velacc to calculate the diffusion coeficient for my solute. For this, I performed a simple simulation to test such tool. 1000 water molecules, NPT ensemble positions and velocities colected every 0.01ps Gromacs 4.5. However, once I run: g_velacc -f traj

[gmx-users] g_clustsize not recognize the -mol option and ignore the index file

Hello everybody, I'm using g_clustsize to analyze clusters formed in my solution. However I noticed that not would get consistent results using the complete trajectory (containing both solvent and solute). To see the aggregation, using g_clustsize, I had to convert my trajectory to a file

[gmx-users] g_wham: Pull geometry direction_periodic not supported

Hi gmx-users I finished a series of pulling runs using the periodic_direction option and when I run the g_wham analysis I received the following message. --- Program g_wham, VERSION 4.5 Source code file: gmx_wham.c, line: 1369 Fatal error: Pull

[gmx-users] Dipeptide generation problem

Hello everybody, I'm trying to create a dipeptide (L-PHE-L-PHE) from the PHE CHARMM residue. This dipeptide has a positively charged site (NH3+) and a negatively charged site (COO-). My PDB file ( https://sites.google.com/site/fileti/ ) does not seem to be consistent and produces error when I

Re: [gmx-users] Dipeptide generation problem [Justin]

+55.11.4996-0196 http://fileti.ufabc.edu.br -- Message: 2 Date: Thu, 26 Aug 2010 09:32:06 -0300 From: Eudes Fileti fil...@ufabc.edu.br Subject: [gmx-users] Dipeptide generation problem To: gmx-users@gromacs.org Message-ID: aanlktikwxuc1g8fq

RE: RE: [gmx-users] Dipeptide generation problem [Justin, Mark, Osmair]

users gmx-users@gromacs.org Message-ID: fb1e9b59.4c772...@anu.edu.au Content-Type: text/plain; charset=iso-8859-1 - Original Message - From: Eudes Fileti fil...@ufabc.edu.br Date: Friday, August 27, 2010 2:15 Subject: Re: [gmx-users] Dipeptide generation problem [Justin] To: gmx

Re: [gmx-users] Charmm to Gromacs: Polyols force field [Justin]

(Eudes Fileti) 3. Re: Charmm to Gromacs: Polyols force field (Justin A. Lemkul) 4. PMF (abdul wadood) 5. Re: please, how edr data is xdr packed? (Sander Pronk) -- Message: 1 Date: Sun, 22 Aug 2010 17:52:46 +0200 From

Re: Re: [gmx-users] Charmm to Gromacs: Polyols force field [Justin]

Hello Justin, thanks again. Well, the line 40 is just one of the 36 parameters not found! In this link ( https://sites.google.com/site/fileti/ ) I put the complete files. I know I need to determine which bond type should be called and I believe that it has been done, but I don't know why it's not

Re: Re: Re: [gmx-users] Charmm to Gromacs: Polyols force field [Mark]

Hello Mark thanks for the comments, In fact, what I did was insert the parameters into ffbonded.itp file. What I presented the link above is just the part that I had added (of course there is the line 1495, not shown!). The installation where I started making the change is new, I have not changed

Re: Re: Re: [gmx-users] Charmm to Gromacs: Polyols force field [Mark, Justin]

Olá, Mark and Justin. Solved. I did what you suggested and I got all the default values. Muito obrigado! eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP

[gmx-users] Charmm to Gromacs: Polyols force field

Olá pessoal, Recently, McKerrel published his CHARMM force field to polyols (JCTC, 2009, 5, 1315). I am very interested in using it in GROMACS. For this, I began the transfer of the parameters with the following recipe: 1) All atom types were added to the atomtypes.atp file; 2) All bonded

[gmx-users] PMF in vacuum and pull direction (chris.ne...@utoronto.ca)

Hello Chris, thanks for the tips, they were very helpful. Now a new problem appeared. I'm trying to separate the two benzene molecules from one another while maintaining the displacement vector aligned with the z axis. For that I have used pull_geometry = direction. However, at the end of the

[gmx-users] PMF in vacuum and pull direction (chris.ne...@utoronto.ca)

Dear Chris, I'm so sorry for surperficial email. You are correct because in the previous message I forgot to mention that now the simulation was performed in water (naturally with PBC). The main parameters of the simulation are given below. As I said, I wish to keep the displacement of the pulled

[gmx-users] PMF in vacuum and pull direction (chris.ne...@utoronto.ca)

Hello Chris, thanks for the reply. Below his message commented walkthrough. In your email you asked me for quantitative results. All I have so far is a visual inspection of the pulling trajectory. All I can see are the two molecules moving linearly away from each other in a rectangular box of

[gmx-users] Re: PMF in vacuum (chris.ne...@utoronto.ca)

Hello Chris, thanks for your attention. I'm sending you some links to some tests I performed. As I said you will notice that depending on the parameter used my simulation shows PMF profiles quite different. Especially what concerns to the difference between the use or not of the PBC.

[gmx-users] PMF in vacuum

Hi gmx-users, I'm trying to simulate a umbrella sampling PMF between two benzene molecules in vacuum. My protocol is working fine, my histograms have good overlap and the curves I have got are quite reasonable. However I have noticed that some options in my .mdp file can significantly change the

[gmx-users] Restraints of COM

Hello everybody, I have two benzene molecules and I want to restrain them only by their center of mass. The conversation below (between Shirts and Spoel) gave me some ideas but still I couldnt solve the problem. In particular I'm not seeing any way to create this user group, nor how to calculate

[gmx-users] Restraints of COM 2

Hello everybody, I have two benzene molecules and I want to restrain them only by their center of mass. The conversation below (between Shirts and Spoel) gave me some ideas but still I couldnt solve the problem. In particular I'm not seeing any way to create this user group, nor how to calculate

[gmx-users] LJ(SR), positive for water

Hello everybody, anyone could help me and understand why the LJ energy is positive for SOL-SOL interactions? The same is not true for LJ energy between benzene (BEN-BEN) and acetonitrile (ACN-ACN). In my opinion it should be negative considering the analytical form LJ potential. Epot (kJ/mol)

[gmx-users] Angle between normal of rings at same molecule

Dear gmx-users, I have a molecule with two rings and would like to calculate the angle between the normal vector of these rings. Anyone have idea of how this can be done? eef __ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do

[gmx-users] Decoupling of Coul. and LJ separately in free energy calculation

Dear GMX users, it is recommended the use of two-step procedure for decoupling the solute from the solvent in hydration free energy calculation: first decreasing the charges in the solute, without soft core, and after that, the same procedure is used for the LJ interactions. In version Gromacs 4,

[gmx-users] PBC screw

Hello, grompp 4.0.5 gave me the following error message. ERROR: invalid enum 'full' for variable pbc, using 'xyz' Next time use one of: 'xyz' 'no' 'xy' 'screw' Could someone tell me what does the screw option? I cant find it into paper and online manual, as well as at the gmx-list. bests eef

[gmx-users] Enthapy of vaporization for aromatics

Hello gmx users. I have tried to calculate the enthalpy of vaporization of toluene liquid, which is about 38kJ/mol (exp. value) using the OPLS-UA model (7 sites). I generated the toluene topology adapting a template provided by PRODRG. I have obtained acceptable value for density and structure of

[gmx-users] Re: Normal of the benzene and z axis.

Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4437-0196 http://fileti.ufabc.edu.br On Tue, Jun 2, 2009 at 9:01 AM, Eudes Fileti fil...@ufabc.edu.br wrote: Dear gmx users;How can I calculate the angle distribution forthe angle

[gmx-users] Re: Re: Normal of the benzene and z axis.

CEP 09210-971 +55.11.4437-0196 Message: 5 Date: Wed, 3 Jun 2009 09:08:43 -0300 From: Eudes Fileti fil...@ufabc.edu.br Subject: [gmx-users] Re: Normal of the benzene and z axis. To: gmx-users@gromacs.org Message-ID

[gmx-users] Normal of the benzene and z axis.

Dear gmx users;How can I calculate the angle distribution forthe angle between the normal of the benzene and z axis? Bests eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP

[gmx-users] RDF in GMX 4

Hello, everyone, in earlier versions of the Gromacs the option to calculate rdf between center of mass (com-com) was not implemented. Is this option implemented in version 4.0? If no, someone would have suggestion to calculate the RDF com-com for liquid benzene? thanks EEF

[gmx-users] RE: RE: RDF in GMX 4 (Justin)

Thanks for reply Justin. I had already read this part of the manual but I can´t understood it well. How can I take account the mentioned input file run? Would it be a kind of index file? Could you provide me an example? Bests eef ___ Eudes Eterno Fileti Centro

[gmx-users] Hydrogen bonds from interface - gOH(z)

Hi everyone, I am working with water in interface with air and I would examine how the hydrogen bonds vary with the distance from the interface. Something like that (

[gmx-users] Re: Softcores: sc-power = 1 or 2 ? again (Berk and Justin)

Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC Rua Santa Adélia, 166 - Bloco B, Sala 1048 09210-170 Santo André - SP Brasil +55.11.4437-8408 skype: eefileti http://cromo.ufabc.edu.br/~fileti/ On Wed, Mar 18, 2009 at 11:44 AM, Eudes Fileti fil...@ufabc.edu.br wrote: Berk

[gmx-users] RE: Softcores: sc-power = 1 or 2 ? again (Berk Hess)

...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. RE: Softcores: sc-power = 1 or 2 ? again (Eudes Fileti) 2. RE: Softcores: sc-power = 1 or 2 ? again (Berk Hess

[gmx-users] Softcores: sc-power = 1 ou 2 ?

Hello, I have a doubt regarding the use of soft-core. When the use of sc-power = 2 is more recommended than sc-power = 1? eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC Rua Santa Adélia, 166 - Bloco B, Sala 1048

RE: [gmx-users] Softcores: sc-power = 1 or 2 ? again

Hello Berk, I have tried to calculate the free energy of transfer for a polyhydroxylated (from benzene to ethanol). The Dg/dlambda plot, for both, benzene and ethanol shows a very high and narrow peak near lambda=0. In the case of ethanol is worse due to the solute-solvent hydrogen bonds. I

Re: [gmx-users] Diffusion coefficients ( Exp X Simul )

Subject: Re: [gmx-users] Diffusion coefficients ( Exp X Simul ) To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 49ada3f0.4090...@xray.bmc.uu.se Content-Type: text/plain; charset=ISO-8859-1; format=flowed Eudes Fileti wrote: Hello, someone could suggest me references which

[gmx-users] Diffusion coefficients ( Exp X Simul )

Hello, someone could suggest me references which discusses the difficulty of obtaining values for diffusion coefficients in agreement to the experimental values? For water that is well known, but I do not know of any reference that discusses this topic Thanks eef

[gmx-users] CO2 Linear triatomic - topology problem

Hi gmx-users, I am trying to build a CO2 topology. Because CO2 is a triatomic linear molecule there is a discontinuity in the potential for the angle of 180 degrees, so I must use virtual sites to circumvent the problem. I have create my topology (gave below) from arguments I read in the forum

Re: [gmx-users] Free energy of transfer with accuracy

Hello David, thanks for the reply! I am simulating the free energy of transfer of the C60, from ethanol to benzene. The softcore parameters, I used the are the same values of Tieleman et.al. (nature nanotechnology, 3, 363). At figure, each curve refers to a different solvent; one of them for

Re: [gmx-users] Free energy of transfer with accuracy

] Content-Type: text/plain; charset=ISO-8859-1 Eudes, On Thu, Dec 11, 2008 at 8:27 AM, Eudes Fileti [EMAIL PROTECTED] wrote: Hello David, thanks for the reply! I am simulating the free energy of transfer of the C60, from ethanol to benzene. The softcore parameters, I used the are the same values

[gmx-users] Free energy of transfer with accuracy

Hi gmx-users, I have tried to calculate the free energy of transfer of a solute between two solvents by thermodynamic integration. However, the dgdl plot I have obtained is not smooth enough to ensure accuracy. I have used a non homogeneous spacing for lambda. The first is from 0.0 to 0.4

[gmx-users] How long should I run a free energy simulation

Hi all,I am performing some free energy test calculations for benzene in water. How long should I run a simulation so that I get reliable result on my test? Thanks eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC Rua

[gmx-users] Re: Constraints - PMF - Different Molecules (Mark Abraham/Arthur Roberts)

Dear Mark and Arthur, thank you for your reply. I did what you suggest me and almost everything worked. I created a topology with the two molecules without bonded parameters between them and put constrains on two of its atoms. I did a minimization and a simulation (md integrator). It worked

[gmx-users] Re: Constraints - PMF - Different Molecules

Hi Mark, sorry, but could you be more specific whenyou say Combine the topologies? Was not it what I had done early? Thank you eef The error you report is potentially of the everyday http://wiki.gromacs.org/index.php/blowing_up variety. See

[gmx-users] Re: Constraints - PMF - Different Molecules (Mark Abraham)

Hello Mark, thanks for your attention. I had already made some attempts setting the two molecules in the same block (as suggested in the forum) but I had no success. I tried to use restraints and constraints and but run always fails. Please I am sending my .mdp and .top files as well as the

[gmx-users] Re: Free energy - Hydrogen bond solute-solvent - Ethanol as an example.

Hello all I have tried to reproduce the hydration free energy (TI) of the ethanol from Hess and van der Vegt (JPCB, 110, 17616). The value I have obtained is around 20kJ/mol while the reference value is -20.1kJ/mol (if not the sign ...). If someone can help me find the mistake I

[gmx-users] Free energy - Hydrogen bond solute-solvent - Ethanol as an example.

Hello to all I have tried to reproduce the hydration free energy (TI) of the ethanol from Hess and van der Vegt (JPCB, 110, 17616). The value I have obtained is around 20kJ/mol while the reference value is -20.1kJ/mol (if not the sign ...). If someone can help me find the mistake I would be very

Re: [gmx-users] Infinite system PBC and Bonded Interaction

always to update the Gromacs. I am using version 3.3.3 and errors still occur. Someone would have any suggestions? Thanks eef On Fri, Apr 25, 2008 at 10:31 AM, Eudes Fileti [EMAIL PROTECTED] wrote: Dear Mark, thank you for your reply and suggestion. I was forgetting the follow detail

Re: [gmx-users] Infinite system PBC and Bonded Interaction

Abraham [EMAIL PROTECTED] Subject: Re: [gmx-users] Infinite system PBC and Bonded Interaction To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed Eudes Fileti wrote: I am simulating a infinite

[gmx-users] Infinite system PBC and Bonded Interaction

I am simulating a infinite graphene sheet in water. The expected is that the system it is infinite in xy plane. But after the simulation I note that the edges of the box (in particular the graphene) are not replicables, i. e., it do not match with its images. I suspect that I may be wrong in using

[gmx-users] Tools for axial symmetry

Dear colleagues I have made simulation of infinite nanotubes in solvent environment. However I can not use the usual tools of the GROMACS to analyze my simulation (as g_rdf, trajorder, etc) due to axial symmetry (cylindrical). Problem that I need to solve are the calculation of rdf (taking as

[gmx-users] Protonate and OPLS

Dear gmx users The tool protonate also works for the OPLS force field or only for GMX? I tried and I did not obtain sucess! Bests eef -- ___ Eudes Eterno Fileti Centro de Ciência Naturais e Humanas Universidade Federal do ABC Rua Catequese, 242 - 3º Andar

[gmx-users] How can I add hydrogen?

Dear gmx users I run a simulation of the liquid of acetonitrila (OPLS-UA) and I need of the configurations with explicit hydrogen atoms. Somebody could help me add the H atoms to configurations? eef -- ___ Eudes Eterno Fileti Centro de Ciência Naturais e

[gmx-users] Re: gmx-users Digest, Vol 43, Issue 21

users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=utf-8 Hi, On Tuesday, 6. November 2007 18:13, Eudes Fileti wrote: Dear gmx users I run a simulation of the liquid of acetonitrila (OPLS-UA) and I need of the configurations with explicit hydrogen

[gmx-users] Re: Potential energy positive. Can be?

] Subject: Re: [gmx-users] Potential energy positive. Can be? To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed Eudes Fileti wrote: Hi gmx users, I have tried to simulate a box with 1000 molecules

[gmx-users] Re: Potential energy positive. Can be?

: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed Eudes Fileti wrote: Dear Mark, thank you for your reply. For equilibration of the system, firstly I generated a ordinated lattice of 10x10x10 molecules. After, I carried out successive minimization runs (with STEEP

[gmx-users] Potential energy positive. Can be?

Hi gmx users, I have tried to simulate a box with 1000 molecules of toluene and I always have obtained a positive value for the potential energy. I have used three different models of potential (with and without 14 interactions) and all of them provides a positive value for energy. I must be

[gmx-users] Re: gmx-users Digest, Vol 34, Issue 4

Dear gmx users, I have attempted to run the calculation of vacf. I always receive a message Killed when my analysis arrives in one specific frame. I already looked at my trajectory with gmxcheck and it seems ok. I also looked for in the forum for similar problem and I did find anything. What it

[gmx-users] g_sorient to ethanol

Good ideia Dr Hess! Only more thing. I would have to rerun the simulation to make the C atoms of ethanol 1 and 2 (since my C atoms have index 1 and 5)? Or there is another more practical way of change the index of atoms? eef ___ Eudes Eterno Fileti Centro de

[gmx-users] g_sorient. Only for water?

Dear GMX users The tool g_sorient is applicable only when the solvent is the water? I have attemped to apply it for the case of solvation in ethanol and I am not obtaining an appropriate vector for the calculation of the angle. In fact, it woul be very nice if I can make the C=C bond of ethanol

[gmx-users] g_sorient. Again.

Dear Berk, Thank you for the reply. Actually my problem is not related to the analysis of bonds but of angles. Specifically, I am interested in the distribution of the angle I between the C=C bond of etanol with a plan of my solute molecule. It also would be interesting to analyze as this angle

[gmx-users] Re: gmx-users Digest, Vol 33, Issue 70

Fatal error: Something wrong with contents of index file. you may need to add the -type flag, run g_sgangle -h -- David. Sorry David, but seems that the g_sgangle utility has not this option. eef ___ Eudes Eterno Fileti Centro de Ciência Naturais e

[gmx-users] Re: gmx-users Digest, Vol 33, Issue 69

I am trying to calculate the angle between two plans. For this I created an index file with all triples of atoms related to each plan. Thus I would get the angle between the normal of these plans. To get the index file I used: mk_angndx -s topol.tpr -n angle.ndx To calculate the angles I used

[gmx-users] Calculation of the angle between planes: g_sgangle

Dear gmx users I am trying to calculate the angle between two planes. For this I created an index file with all triples of atoms related to each plane. Thus I would get the angle between the normal of these planes. To get the index file I used: mk_angndx -s topol.tpr -n angle.ndx To calculate

[gmx-users] How can I generate a FCC unit cell?

Hi gmx-users, I need to generate a FCC unit cell (in fact a face centered cubic lattice) in order to produce a nanocristal. I would like to know if is possible to make this using directly GROMACS. In affirmative case, as I can make it? Thanks in advance ___

[gmx-users] Buckingham model for liquid of water

Dear gmx-ersI have attemped to use the potential of Buckingham to simulate the water liquid. However I did not find papers that present the parameters of the potential. Actually I found a paper that mixed parameters LJ (O...O) and Buckingham (O-H, O-O and H...O). Can anyone let me know if there is

[gmx-users] Internal coordinates to the topology

Dear gmx-userI have a crystalline cell with 150 atoms. Somebody would know to say me as to generate the pairs (bond), triples (angles) and quaternios (dihedral) for the topology?Is there a good program to do this? For smaller molecules the Gaussian works finebut in this case its fails. I already

[gmx-users] Uncorrelated configurations

Dear Gmx Users I have one trajectory of 800ps. I need extract of this trajectory, only the uncorrelated (statistically independent) configurations. So I need know how many ps separates two consecutive configuratios. Which procedure I can use for this analysis? Thanks eef

[gmx-users] Re: gmx-users Digest, Vol 28, Issue 42

Dear David Actually I posted my doubt in Vol 28, Issue 38. There I detailed more. Anyway, my system is 1 C60 molecule in 1000 ethanol molecules. As said, I need of structures that do not remember the previous one, i.e. that are structural and statistically not correlated. For this, up to now, I

[gmx-users] Benzene and normal modes

Dear GMX usersI think that this question already is old but Could anyone tell me as I could simulate a benzene molecule fixed by its center (at the center of the box) but with its vibration normal modes free?__Eudes Eterno FiletiCentro de Ciência Naturais e

[gmx-users] Problems with the Dihedral of the Ethanol

Dear gmx users I have attemped to simulate a box of ethanol in normal conditions of temperature and pressure. I reproduced very well some literature data (as g(r)) however I had problems to reproduce the angulardistribution function for the dihedral (C-C-O-H). This angle must have a peak in 180

[gmx-users] Label of the atoms in ffoplsaabon.itp

Dear Gmx users:I am a new user and I have some questionsSomebody could say me what it means the index at atoms in the ffoplsaabon.itp file (a fragment of fileis gave bellow). Some are obvious (OH, is oxygen bonden to hydrogen and HO is a hydrogen bonded to oxygen) but definitively I dont know what