[gmx-users] cut-off g_hbond

Hi all I am using g_hbond to calculate the number of hydrogen bonds in an alcohol system. I am using the following command: g_hbond -f traj.trr -nonitacc I am slightly confused about the cut off r. Using the above command, is the default cut-off r (0.35nm) for the donor-acceptor distance or the

Re: [gmx-users] cut-off g_hbond

Hi Justin Thanks, that's what I thought. Is there a need to define a hydrogen-acceptor distance as well. I read in a few articles that this was the case, usually 0.25nm ? Cheers Gavin Justin Lemkul wrote: On 10/5/12 7:20 AM, Gavin Melaugh wrote: Hi all I am using g_hbond to calculate

Re: [gmx-users] cut-off g_hbond

Is there any need to use the r2 option the ? Justin Lemkul wrote: On 10/5/12 7:39 AM, Gavin Melaugh wrote: Hi Justin Thanks, that's what I thought. Is there a need to define a hydrogen-acceptor distance as well. I read in a few articles that this was the case, usually 0.25nm ? One can

Re: [gmx-users] cut-off g_hbond

O.K thanks Justin Lemkul wrote: On 10/5/12 8:15 AM, Gavin Melaugh wrote: Is there any need to use the r2 option the ? That option is not relevant here. It is undocumented in the current release, but the help description has been updated for the next release: http://redmine.gromacs.org

[gmx-users] g_hbond

Hi I have an alcohol system and I want to calculate the number of H bonds during the trajectory. My atom type labels are C2-C2-C2-CO-OH-HO. CO denotes carbon bonded to oxygen, OH denotes alcohol oxygen, and HO denotes alcohol hydrogen. In g_hbond how do I specify my groups to consider for H

[gmx-users] wham histograms

Hi all Are the histograms from histo.xvg (output of g_wham) the biased or unbiased distributions? Cheers Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] extra factor in PMF

Hi all According to some references 1) J. Chem. Phys, 128, 044106, (2008) 2) Comparison of Methods to Compute the Potential of Mean Force Daniel Trzesniak, Anna-Pitschna E. Kunz, Wilfred F. van Gunsteren Prof. Article first published online: 28 NOV 2006 DOI: 10.1002/cphc.200600527 There is

[gmx-users] DD load balancing is limited by minimum cell size in dimension Z

Hi all What does the following note mean in the log file DD load balancing is limited by minimum cell size in dimension Z Is is purely a performance related issue ? Cheers Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

[gmx-users] genbox

Hi all I have a system of 40 solute molecules in a solvent of 480 crown ether molecules. I am not trying to insert 100 methane molecules into this relaxed and well equilibrated structure using genbox. There are clearly visible cavities in the fluid but genbox only alllows the insertion of 8

[gmx-users] fatal error

Hi all I am trying to relax the density of an alcohol system that I have just set up, but after a certain period of time I get the following error Fatal error: The X-size of the box (6.800588) times the triclinic skew factor (1.00) is smaller than the number of DD cells (4) times the smallest

[gmx-users] bug in g_msd

Hi all Is there a bug with g_msd when using the -mol flag. I have my own program that calculates the MSD. If I compare it with the gromacs utility for one system the curves are the exact same, however when I compare with another system th curves are very different. Someone else mentioned

[gmx-users] [Fwd: bug in g_msd]

---BeginMessage--- Hi all Is there a bug with g_msd when using the -mol flag. I have my own program that calculates the MSD. If I compare it with the gromacs utility for one system the curves are the exact same, however when I compare with another system th curves are very different. Someone

[gmx-users] g_msd segmentation fault

Dear All I have a system of 40 solute molecules in 480 crown ether solvent molecules. When I ran the msd analysis on the solvent molecules using the following comand. g_msd_login_d -f traj.trr -s topol.tpr -mol -o 1_12_400K_sol_msd.xvg I get a segmentation fault as follows Select a group: 4

[gmx-users] folding of coordinates in trajectory files

Hi All I was wondering. I assume gromacs writes folded coordinates in the trajectory files. If so does it use rx(i) = rx(i) -boxl *nint(rx(i) / boxl) to fold the coordinates at each step? and where does it define the origin (0,0,0) Cheers Gavin -- gmx-users mailing list

Re: [gmx-users] Error note

Hi Justin I saw this and had a question. How important is it for a charge group to be neutral? In one of my systems I model a solvent of crown ethers using an all atom model. The smallest neutral unit comprises a CH2-O-CH2 (7 atoms). I have used this as a charge group to and get no warnings.

Re: [gmx-users] Error note

I am using 4.5.5 Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin I saw this and had a question. How important is it for a charge group to be neutral? It isn't. Conventional use dictates that the charge group bear an integral charge. With PME, this is not necessary. Many force

[gmx-users] pull-code

Hi all I am returning to a query I had a few weeks ago regarding a discrepancy between two free energy curves. One calculated using umbrella sampling, the other calculated via the reversible work theorem from the RDF. There is sufficient sampling of the dynamics in the RDF so this method is

Re: [gmx-users] pull-code

Hi Thomas Many thanks for the reply again. At larger distances the two curves match up quite well. The curve from the reversible work theorem is better behaved and smoother but this could be solely due to statistics. I am slightly confused about your statement If the small circle moves between 0

Re: [gmx-users] pull-code

Hi Thomas I am sorry to bother you but if you could answer a few questions I have about how the pull-code works with respect to my system I would really appreciate it. My system is a liquid and I am trying to pull one substituent of one liquid molecule in a certain region of another liquid

Re: [gmx-users] RDF(PMF) and Umbrella sampling

nm to -0.02nm. What happens to negative values? Obviously they are not counted as negative in the distribution or else it would be centred at zero/ Cheers Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin Thanks very much. One last question. What do you mean when you say COM

Re: [gmx-users] RDF(PMF) and Umbrella sampling

to -0.02nm. What happens to negative values? Obviously they are not counted as negative in the distribution or else it would be centred at zero/ Cheers Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin Thanks very much. One last question. What do you mean when you say COM

[gmx-users] RDF(PMF) and Umbrella sampling

Dear all I have a query regarding umbrella sampling simulations that I have carried out to study a dynamical process of a guest inserting into a host. I always get get a wall tending off to infinity at or just before the zero distance between the two species. The process I describe, for one

Re: [gmx-users] RDF(PMF) and Umbrella sampling

between the COG of the ref group and that of the pull group. Cheers Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Dear all I have a query regarding umbrella sampling simulations that I have carried out to study a dynamical process of a guest inserting into a host. I always get get a wall

Re: [gmx-users] RDF(PMF) and Umbrella sampling

A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin Thanks for the reply. I wanted my pulling to be free in all directions, that is in the liquid state with no defined reaction coordinate i.e not along a specific axis. This is why I used geometry = distance. Would you agree with this approach

Re: [gmx-users] RDF(PMF) and Umbrella sampling

arose for me: why did you consider the (rate = 0)? Dariush On Fri, Jan 6, 2012 at 11:47 AM, Gavin Melaugh gmelaug...@qub.ac.uk mailto:gmelaug...@qub.ac.uk wrote: Hi Justin Just a quick clarification regarding my previous point. With geometry = distance, and pull_dim =Y

[gmx-users] [Fwd: h-bonds constraints]

---BeginMessage--- Hi I want to run an NPT simulation with all h-bonds constrained. How does grompp identify the Hydrogen atoms given that forcefield labels like HA, HC, HE are used. Is it the mass? Many Thanks Gavin ---End Message--- -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] h-bonds constraints

Hi I want to run an NPT simulation with all h-bonds constrained. How does grompp identify the Hydrogen atoms given that forcefield labels like HA, HC, HE are used. Is it the mass? Many Thanks Gavin -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] discrepancy trjconv and gmxdump

Hi all I have generated a gro file from a traj.trr file using trjconv. When I use gmxdump on the same traj.trr file to output a generic format history file it seems that there is a discrepancy in the coordinates of some atoms in a particular frame. Essentially I output frame 5 using trjconv, then

Re: [gmx-users] discrepancy trjconv and gmxdump

file) and pay attention to the sign difference of the x coordinate at atom s 38 50 51 59 Cheers Gavin Mark Abraham wrote: On 2/11/2011 10:23 PM, Gavin Melaugh wrote: Hi all I have generated a gro file from a traj.trr file using trjconv. When I use gmxdump on the same traj.trr file to output

Re: [gmx-users] discrepancy trjconv and gmxdump

Actually Mark, I may have made a very trivial error. Forget about it for now. Cheers Gavin Gavin Melaugh wrote: Hi Mark My Apologies. Here is more info. gmxdump -f traj.trr history From history I take the coordinates at 250 ps and convert to gro file say test.gro trjconv -f traj.trr

[gmx-users] (no subject)

Hi all A very quick question. If I want to constrain all bonds in my system, is it just a case of setting constraints = all-bonds. Do I have to select the constraint algorithm. Here is my mpd file, I got no errors but its seems that this might be too simple. Note there is no relevance in the

[gmx-users] bond constraints

Hi all Sorry forgot to give a subject in the first e-mail. A very quick question. If I want to constrain all bonds in my system, is it just a case of setting constraints = all-bonds. Do I have to select the constraint algorithm. Here is my mdp file, I got no errors but its seems that this might

Re: [gmx-users] atom types

of interaction are written to the log file. Therefore does gen_pairs= yes + [pairs] directive generate 1,4 LJ and 1,4 Coulomb according to fudge LJ and QQ? Thanks Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin Sorry to labour on this but: I don't quite understand what you mean when you

Re: [gmx-users] atom types

wrong? In my set up then, are 1-4 Coulombic interactions determined by the pair list and fudge QQ? Many Thanks Gavin Mark Abraham wrote: On 02/08/11, *Gavin Melaugh * gmelaug...@qub.ac.uk wrote: Hi Justin Again thanks for the reply. I am not disagreeing with you but If I don't include

Re: [gmx-users] atom types

with fudge LJ and QQ. My point is, then in conclusion, that in this way surely the 1,4 electrostatic interactions are determined by the pair list and in my case gen_pairs = yes no? Many Thanks Gavin Mark Abraham wrote: On 02/08/11, *Gavin Melaugh * gmelaug...@qub.ac.uk wrote: Hi Mark

[gmx-users] to clear up the confusion regarding fudge LJ and QQ

Gavin Gavin Melaugh wrote: Yes I think the example vindicates what I am saying as well. I suppose I the contradiction ( I'll call it the point of confusion) you refer to is perhaps when Justin (who is always more than helpful) said that Charges are irrelevant for generation of pair interactions

Re: [gmx-users] atom types

question should have been: Does mdrun, when calculating the Coulombic potential between these two atoms, use the charges assigned to the atoms in the [atomtypes] directive or [atoms] directive ? Cheers Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Yes I think the example vindicates what

Re: [gmx-users] atom types

I hope this doesn't come across as stupid, or worse insolent. But what is the point in stating the charges in the atom type section then ? Gavin Mark Abraham wrote: On 02/08/11, *Gavin Melaugh * gmelaug...@qub.ac.uk wrote: Hi Justin I see that we may have got our wires crossed from the off

[gmx-users] atom types

Hi all A very quick question. I have an atom-type labelled CH in the atom-types with a particular charge, and in the atom list I assign some of these specific atoms with zero charge as below. When I generate 1,4 interactions using gen_pairs =yes, what charge for the CH type does it use? Does

Re: [gmx-users] atom types

gen_pairs = yes, does grompp then take the 1-4 coulombic interaction for CH from the [atomtypes] directive (as the meaning of gen_pairs =yes)? Or does it assign the charge based on the atom index in the pair list? Many Thanks Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi all A very

Re: [gmx-users] atom types

are the 1-4 Coulombic interactions generated by, if not by gen_pairs =yes in my case? I have read this section of the manual loads and though I had a comprehensive understanding of it, but now I am confused again. Thanks Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin I have

[gmx-users] lattice Coulomb energy between energy groups

Hi all I have set up a simulation with PBC using PME and specify an energy group enclusion involving some virtual sites and a hydrocarbon chain. i.e. hydrocarbon chain is one energy group and the virtual sites constitute the other group. Grompp generates the following warning Can not exclude the

Re: [gmx-users] lattice Coulomb energy between energy groups

Hi Justin Thanks for the reply. I take it then, if I use the maxwarn option, it will still apply the exclusion for the short-range non-bonding interactions. Cheers Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi all I have set up a simulation with PBC using PME and specify an energy

[gmx-users] convergence

Hi all I have generated a PMF curve over 15 ns. Does g_wham have a facility whereby I can calculate the PMF over say 7 ns, to check for convergence. There doesn't seem to be anything in the manual. Many thanks Gavin -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] Re: convergence

Please ignore my last question, I have found the answer using the g_wham -h option Cheers Gavin Gavin Melaugh wrote: Hi all I have generated a PMF curve over 15 ns. Does g_wham have a facility whereby I can calculate the PMF over say 7 ns, to check for convergence. There doesn't seem

[gmx-users] error bars g_wham

Hi all I have read the manual and the recent JCTC paper on g_wham, and I was wondering how to actually get the error bars on the profile.xvg file outputted from g_wham. Many Thanks Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

Re: [gmx-users] Re: distance/direction PMF

. I say varying as I don't think the dynamics constrain the pull group alone that vector alone. When you change the vector in the mdp file to be that of the new vector connecting the two groups grompp gives the actual distance between the two groups. Gavin Justin A. Lemkul wrote: Gavin Melaugh

[gmx-users] fatal error

Hi all Why is pull geometry direction not supported in g_wham ? I got the following error. I did this to compare with the same simulations but with pull geometry = distance. Fatal error: Pull geometry direction not supported -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] distance/direction PMF

Hi all Could someone please get back to me on this. I have ran two sets of umbrella sampling simulations 1- Using pull_geometry = distance, and pull_dim = Y Y Y 2- Using pull_geometry = direction, with pull_vec = 0.462808 0.494125 0.735968 In both cases I wish to calculate the PMF for taking a

Re: [gmx-users] Re: distance/direction PMF

that the vector between the two point changes during the run ? Cheers Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin Many thanks for the reply I know technically I am doing two different things. However due to my starting conifgurations in both cases I would expect similar results

Re: [gmx-users] Re: distance/direction PMF

this distance actually means, as it is not the absolute distance between the reference groups. Also as regards to your second point; what if in the initial configurations the two reference groups do not lie along the stated vector? Cheers Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote

Re: [gmx-users] Re: distance/direction PMF

distance between the two groups. Cheers Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin Sorry maybe I was unclear before with my first point; the specified distance in the mdp file is 0.78nm, which grompp returns back as the ref distance. The distance at the start

[gmx-users] energy conservation

Hi all I have run a very long NVT simulation 500ns of one molecule (220 atoms) to try to assess the fluctuations in a particular event. When I analyse the energies it seems that the conserved quantity drifts significantly. Why would this be? Has it got to do with the thermostat I am using? Please

[gmx-users] pull_vec

Hi all In umbrella sampling simulations: If pull_geometry = direction, and pull_vec is obviously a specified vector, does the distance between the two groups only vary along that vector? i.e Is the umbrella potential only defined along that vector? Many Thanks Gavin -- gmx-users mailing list

[gmx-users] Energy groups

Hi all If I have a topology with set up below (excerpts). And define energy groups in the .mdp file say 'virtsites' and 'endgroup' in correspondence with the index file. Will defining energygrp_exl 'virtsites' and 'endgroup' prevent nonbonding interactions between any atom in either of these

[gmx-users] exclusions

Hi all I am cheking the non binary version topol.tpr form grompp and I was wondering what the following format for the exclusion section signifies? excls: nr=228 nra=1920 excls[0][0..12]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16} excls[1][13..25]={0, 1, 2, 3,

Re: [gmx-users] exclusions

index =1) In the next set do you read the exclusion with respect to atom 1 (actual index =2). and so on Many thanks in advance Gavin Gavin Melaugh wrote: Hi all I am cheking the non binary version topol.tpr form grompp and I was wondering what the following format for the exclusion section

[gmx-users] energy group error

Hi All I have set up a topology file and with virtual sites (exerpts below), whereby my virtual sites only interact with the C3 atoms. I am trying to construct a PMF wrt one particular C3. This atom I do not want to interact with the virtual sites at all. I thought the best way to do this was via

Re: [gmx-users] energy group error

Hi again To rephrase. If I have two atoms constructing a charge group, is it not possible to have one of these atoms constructing an energy group on its own? Cheers Gavin Gavin Melaugh wrote: Hi All I have set up a topology file and with virtual sites (exerpts below), whereby my virtual

[gmx-users] charge groups

Hi all Do atoms belonging to the same charge group have to be indexed consecutively in the topology file or can you have the following. [atoms] 1 CA 1 CGECA 1 -0.1150 12.0110 2 CB 1 CGECB 1 0. 12.0110 3

Re: [gmx-users] charge groups

} cgs[19]={32..33} cgs[20]={34..35} cgs[21]={36..36} cgs[22]={37..38} cgs[23]={39..39} cgs[24]={40..41} cgs[25]={42..42} cgs[26]={43..44} cgs[27]={45..46} Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin The two

Re: [gmx-users] charge groups

O.K cheers I assume that this is irrelevant in vacuum with no cut-offs Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: As you can see atomnr 7 HC should belong to the same charge group (1) as atomnr 12. From the tpr file atomnr 7 (in this file 6) seems to have its own charge group (3

Re: [gmx-users] charge groups

Also. Obviously I arranged the charge groups like this so that they would be neutral, I just didn't realise that the atoms comprising the charge groups had to be in sequence. Justin A. Lemkul wrote: Gavin Melaugh wrote: As you can see atomnr 7 HC should belong to the same charge group (1

Re: [gmx-users] virtual sites

] VS1 C 1 1.0 0.25 VS2 C 1 1.0 0.25 VS2 C 1 1.0 0.25 -- sikandar On Thu, May 5, 2011 at 11:47 AM, Gavin Melaugh gmelaug...@qub.ac.uk mailto:gmelaug...@qub.ac.uk wrote: Hi Justin

Re: [gmx-users] virtual sites set up for topology file

[virtual_sitesn] ;site COG of three hydrogens at window ;site i jkfunc 229740 581 230 1025 551 231 2837 521 Cheers Gavin Gavin Melaugh wrote: Hi Sikandar A couple of questions regarding the virtual sites. 1) Do I have to number the virtual site

Re: [gmx-users] virtual sites set up for topology file

Hi Having tried to run grompp using the data below I keep getting the following error Fatal error: Unknown vsiten type 7 Does anyone know why this might be? Gavin Gavin Melaugh wrote: Hi I am trying to alter a topology to include 3 virtual sites and I have a few queries, the answers to which

Re: [gmx-users] virtual sites set up for topology file

[virtual_site3], site index atom indices, and function 1. The fact that there are no parameters then by default must mean it is COG. Is this correct? Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Having tried to run grompp using the data below I keep getting the following error Fatal

Re: [gmx-users] virtual sites set up for topology file

section to the right molecule. Do I have to have the virtual sites in the gro file also? This doesn't make sense Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin Thanks for the reply. To create a virtual site at the centre of geometry of 3 atoms, according to the manual, do you

Re: [gmx-users] virtual sites set up for topology file

Yeah I see your point about the types. With regard to the initial configuration state I would have assumed that gromacs knew the initial position of the virtual site when I stated that it was to be at the COG of the 3 atoms in the [virtual_sitesn] directive. Justin A. Lemkul wrote: Gavin

Re: [gmx-users] virtual sites set up for topology file

O.k Cheers Justin A. Lemkul wrote: Gavin Melaugh wrote: Yeah I see your point about the types. With regard to the initial configuration state I would have assumed that gromacs knew the initial position of the virtual site when I stated that it was to be at the COG of the 3 atoms

Re: [gmx-users] virtual sites set up for topology file

Hi Mark Cheers.Could you perhaps shed some insight into format of [virtual_siten] when trying to define the VS at the COG of three atoms. It is not obvious from the manual Cheers Gavin Mark Abraham wrote: On 6/05/2011 10:17 PM, Gavin Melaugh wrote: Yeah I see your point about the types

Re: [gmx-users] virtual sites set up for topology file

1 However the function type should be stated before the atom indices comprising the COG ;index of VS func indices 229 1 8 11 15 Cheers Gavin Mark Abraham wrote: On 6/05/2011 10:39 PM, Gavin Melaugh wrote: Hi Mark Cheers.Could

Re: [gmx-users] virtual sites set up for topology file

Am I correct in saying now, from the following topology (exerpts), that the virtual site VS will only interact with C3? I guess I don't have to give the atom indices of this interaction in the pair list which I use only for 1_4 interactions? Can I use sigma and epsilon in the nonbond_params

Re: [gmx-users] virtual sites set up for topology file

sigma(VS_C3) epsilon(VS_C3) you defined under [nonbond_params] cheers sikandar On Fri, May 6, 2011 at 9:03 AM, Gavin Melaugh gmelaug...@qub.ac.uk mailto:gmelaug...@qub.ac.uk wrote: Am I correct in saying now, from the following topology (exerpts), that the virtual site VS

[gmx-users] nrexcl=3

Hi all A very quick question. From the manual the definition of nrexcl =3 is excluding nonbonded interactions between atoms that are no further than 3 bonds away. In say butane does this means that atoms 1 and 4 do not interact, or I take it they interact according to the pair list. Gavin --

[gmx-users] virtual sites

Hi All Is it possible to have a virtual site interact with only specific atoms and not interact at all with everything else? Cheers Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

Re: [gmx-users] virtual sites

, then exclude or include the non-bonded interactions between them accordingly... On Thu, May 5, 2011 at 7:30 AM, Gavin Melaugh gmelaug...@qub.ac.uk mailto:gmelaug...@qub.ac.uk wrote: Hi All Is it possible to have a virtual site interact with only specific atoms

Re: [gmx-users] virtual sites

and exclusions, and list all the indices of the atom types that I don't want to interact with the virtual site in one group and all the virtual sites in another. e.g [virtual sites] 17 18 19 20 [virtsite_exclus] 1 2 3 4 5 6 7 8 9 . Cheers Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi

Re: [gmx-users] virtual sites

to manual.. I hope it helps -- sikandar On Thu, May 5, 2011 at 11:00 AM, Gavin Melaugh gmelaug...@qub.ac.uk mailto:gmelaug...@qub.ac.uk wrote: Hi Sikandar Cheers. How do you actually define the energy groups? Gavin Sikandar Mashayak wrote: yes, you can make

Re: [gmx-users] virtual sites

Hi Justin I do not intend to have charges on the sites. All I want is; when a CH3 group gets close to the site it feels a repulsive force. I have calculated a sigma and epsilon value for this interaction. Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin I am reading the manual

[gmx-users] free energy

Hi all I have performed a PMF simulation of taking part of a molecule out of the cavity of a host using umbrella sampling. The free energy curve suggests that the guest prefers to be outside the host as the bound state is higher in energy, or the free energy difference to go in is positive.

Re: [gmx-users] free energy

Hi Chris My windows are restrained obviously using the force constant in the mdp file. The trajectories that I have viewed are those of the individual biased sampling windows. I have not put on the unbiased simulations yet. There is also the following issue: The simulations involve two identical

Re: [gmx-users] free energy

The current simulations are currently in vacuum. Does the following mdp file seem ok. Note that this is a production run using the final configuration after a lengthy equilibration. Also I was thinking about trying to prevent the other chains from entering the specific site; is there a a way to

Re: [gmx-users] Umbrella Sampling

Hi I assume that the order of the file names in the tpr-files.dat and pullx-files.dat is irrelevant for g_wham . Cheers Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

Re: [gmx-users] Umbrella Sampling

Gavin Justin A. Lemkul wrote: From g_wham -h: The tpr and pullx files must be in corresponding order, i.e. the first tpr created the first pullx, etc. -Justin Gavin Melaugh wrote: Hi I assume that the order of the file names in the tpr-files.dat and pullx-files.dat is irrelevant for g_wham

Re: [gmx-users] Umbrella Sampling

Cheers Chris Is the best way to check for convergence; to keep adding in more histograms until the curves converge. Also your comment 'don't remove any data', do you mean to keep histograms that are not so good. Gavin chris.ne...@utoronto.ca wrote: your comment: which should be centred

[gmx-users] Umbrella sampling

Hi All I have generated several PMF curves for the one system using umbrella sampling. In the first part of the curve (barrier region) I use a high force constant with small intervals between the windows. The latter part of the curve I use a lower force constant with larger window spacing. Anyway

Re: [gmx-users] Umbrella sampling

XAvier Periole wrote: On Mar 31, 2011, at 11:53 AM, Gavin Melaugh wrote: Hi All I have generated several PMF curves for the one system using umbrella sampling. In the first part of the curve (barrier region) I use a high force constant with small intervals between the windows. The latter part

Re: [gmx-users] Umbrella sampling

:)) On Mar 31, 2011, at 12:20 PM, Gavin Melaugh wrote: Hi Xavier Thanks for the reply. With respect to your answer of my first query. What if you had two windows practically on top of each other, but one was not supposed to be there. e.g A window with r0 of 0.80 nm and centred at 0.78 nm

Re: [gmx-users] Umbrella sampling

Thanks Justin for the reply Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Sorry I am not sure that I follow. Will the window with r0 =0.80 giving the distribution centred around 0.78nm not drive my free energy profile up. If I remove this window prior to running g_wham the free energy

[gmx-users] Umbrella Sampling

Hi Chris many thanks again for the advise. I have, or at least I thought have sampled my barrier region to death, but as I say some histograms may not be centred around r0. I will proceed with what you suggest. Please find attached a picture of the histograms, the corresponding profile, and a

Re: [gmx-users] Umbrella sampling

(0.80 nm) are converged :)) On Mar 31, 2011, at 12:20 PM, Gavin Melaugh wrote: Hi Xavier Thanks for the reply. With respect to your answer of my first query. What if you had two windows practically on top of each other, but one was not supposed to be there. e.g A window with r0 of 0.80 nm

Re: [gmx-users] Umbrella Sampling

Cheers Chris If I remove the red histogram (the first of the wider distributions), which should be centred around 0.80nm but is actually centred around 0.78 nm; and add in some more histograms with higher force constants the profile changes slightly. It seems that g_wham is very sensitive to

[gmx-users] pullx.xvg format

Hi all I have a very quick question. The output for umbrella pulling simulations (pullx.xvg) often appears to have an irregular format, in that the columns don't seem to be perfectly aligned (see below). I have never had a problem with this as g_wham never reported any errors. I was just

Re: [gmx-users] pullx.xvg format

Hi Justin Thanks for the reply. I expanded the terminal and it didn't make a difference. Do you still think it's O.K? Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi all I have a very quick question. The output for umbrella pulling simulations (pullx.xvg) often appears to have

[gmx-users] sum of largest charge group radii

Hi I have installed the new version of gromacs and so far I only use it as a check when running grompp as it gnerates more information about cut off charge group radii etc. For a system of 256 hexane molecules in a cubic box I get the following error. WARNING 1 [file pbc.mdp]: The sum of the

Re: [gmx-users] sum of largest charge group radii

Hi Justin By broken do you mean split at the edge of the periodic box? If so then yes. Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi I have installed the new version of gromacs and so far I only use it as a check when running grompp as it gnerates more information about cut off

Re: [gmx-users] sum of largest charge group radii

Then is this a bug?, or do I have to have a box in which all the molecules are whole. Does that not defeat the purpose of having a periodic box? Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin By broken do you mean split at the edge of the periodic box? If so then yes

Re: [gmx-users] sum of largest charge group radii

Yeah I did that and there was no error, cheers. I did the same thing a week a go for a united atom model of hexane, I did not get the warning then even though the molecules were still broken. Peculiar? Justin A. Lemkul wrote: Gavin Melaugh wrote: Then is this a bug?, or do I have to have

[gmx-users] Pull code

Dear All Sorry wrong subject title in previous post. Can someone please tell me how to generated the plot of mean force having ran the pull code at several distances using constraints? Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

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