Re: [gmx-users] g_WHAM

On 8/20/13 9:59 AM, Shima Arasteh wrote: Hi, I have a tpr-files.dat containing 5 tpr files as it: 4.tpr 5.tpr 6.tpr 7.tpr 8.tpr Also the pullf-files.dat is in accordance with tpr-files.dat. But when I run g_wham and visualize the histo output, I see only one curve and not 4 curves which a

[gmx-users] g_WHAM

PM Subject: Re: [gmx-users] g_WHAM On 8/8/13 2:37 PM, Shima Arasteh wrote: > g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCalvv > > It's the error what get; > File input/output error: > tpr-files.dat > Then a file named "tpr-files.dat" does n

Re: [gmx-users] g_wham error analysis hangs

Hi Jochen, Seems as if this error was associated with the mpi version. Everything worked ok when running it locally. Best regards / Magnus On Aug 12, 2013, at 1:50 PM, Jochen Hub wrote: > Hi Magnus, > > I just read your mail. Sound very much like a bug, which never occurred > to me though.

Re: [gmx-users] g_wham error analysis hangs

Hi Magnus, I just read your mail. Sound very much like a bug, which never occurred to me though. But I did not use -bs-method traj-gauss a lot. Does the error also occur with -bs-method traj? Btw: with -bs-method traj-gauss or traj, you need realistic estimates of the autocorrelation times (ACTs)

Re: [gmx-users] g_wham -sym

t; - Original Message - > From: Justin Lemkul > To: Shima Arasteh ; Discussion list for GROMACS > users > Cc: > Sent: Friday, August 9, 2013 2:40 PM > Subject: Re: [gmx-users] g_wham -sym > > > > On 8/9/13 5:48 AM, Shima Arasteh wrote: >> Hi, >> >

Re: [gmx-users] g_wham -sym

: [gmx-users] g_wham -sym On 8/9/13 5:48 AM, Shima Arasteh wrote: > Hi, > > I use the > g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kca -sym > > > I' d like to know if it is possible to symmetrize the profile around a > non-zero point? forexample z

Re: [gmx-users] g_wham -sym

On 8/9/13 5:48 AM, Shima Arasteh wrote: Hi, I use the g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kca -sym I' d like to know if it is possible to symmetrize the profile around a non-zero point? forexample z=60? Use -zprof0. -Justin -- ===

[gmx-users] g_wham -sym

Hi, I use the  g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kca -sym I' d like to know if it is possible to symmetrize the profile around a non-zero point? forexample z=60? Thanks for your suggestions in advance.   Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs

Re: [gmx-users] g_WHAM

xistence of the file. -Justin Sincerely, Shima - Original Message - From: Justin Lemkul To: Shima Arasteh ; Discussion list for GROMACS users Cc: Sent: Thursday, August 8, 2013 10:45 PM Subject: Re: [gmx-users] g_WHAM On 8/8/13 2:13 PM, Shima Arasteh wrote: Hi, Would you please

Re: [gmx-users] g_WHAM

13 10:45 PM Subject: Re: [gmx-users] g_WHAM On 8/8/13 2:13 PM, Shima Arasteh wrote: > Hi, > > Would you please let me know if it is possible to get just the first 2 > histograms of total 24 histograms by running g_WHAM? > I mean the tpr-files.dat contains only 2 .tpr files

[gmx-users] g_WHAM

Hi, Would you please let me know if it is possible to get just the first 2 histograms of total 24 histograms by running g_WHAM? I mean the tpr-files.dat contains only 2 .tpr files of umbrella sampling simulations and not the all. I ran such dat file, but doesn't work and gives me an error of n

Re: [gmx-users] g_WHAM

On 8/8/13 2:13 PM, Shima Arasteh wrote: Hi, Would you please let me know if it is possible to get just the first 2 histograms of total 24 histograms by running g_WHAM? I mean the tpr-files.dat contains only 2 .tpr files of umbrella sampling simulations and not the all. I ran such dat file,

Re: [gmx-users] g_wham error analysis hangs

On 8/5/13 8:21 AM, Magnus Andersson wrote: What version of Gromacs are you using? How many data points do you have in the full set? -Justin Gromacs 4.6 not sure what you mean by data points, but: dt = 0.002 nsteps = 100 Not relevant, but

Re: [gmx-users] g_wham error analysis hangs

> What version of Gromacs are you using? How many data points do you have in > the full set? > > -Justin > Gromacs 4.6 not sure what you mean by data points, but: dt = 0.002 nsteps = 100 and total number of atoms in the system: 265,891 # frames

Re: [gmx-users] g_wham error analysis hangs

On 8/5/13 8:06 AM, Magnus Andersson wrote: I've had this happen before when trying to analyze too many data points. Try reducing the size of the input data using -b to see if that helps. -Justin Thanks for the suggestion, Justin. However, either it hangs or I get: Fatal error: Tryig to

Re: [gmx-users] g_wham error analysis hangs

> > I've had this happen before when trying to analyze too many data points. Try > reducing the size of the input data using -b to see if that helps. > > -Justin Thanks for the suggestion, Justin. However, either it hangs or I get: Fatal error: Tryig to estimtate autocorrelation time from on

Re: [gmx-users] g_wham error analysis hangs

On 8/5/13 2:29 AM, Magnus Andersson wrote: Hi, I have a problem with the error analysis of g_wham. The PMF profile and sampling windows looks good, but when I try to generate error bars g_wham hangs. This is what I do: g_wham_mpi -if pullf-files.dat -it tpr-files.dat -o -hist -nBootstrap 5

[gmx-users] g_wham error analysis hangs

Hi, I have a problem with the error analysis of g_wham. The PMF profile and sampling windows looks good, but when I try to generate error bars g_wham hangs. This is what I do: g_wham_mpi -if pullf-files.dat -it tpr-files.dat -o -hist -nBootstrap 50 -bins 50 -bs-method traj-gauss -bsres -ac y

Re: [gmx-users] g_wham missing option

-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: 02 February 2013 18:06 To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_wham missing option On 2/2/13 12:58 PM, Nash, Anthony wrote: Hi All, I am using Gromacs 4.5.5 and

RE: [gmx-users] g_wham missing option

: Discussion list for GROMACS users Subject: Re: [gmx-users] g_wham missing option On 2/2/13 12:58 PM, Nash, Anthony wrote: > Hi All, > > I am using Gromacs 4.5.5 and running free energy calculations. According to > the article "g_wham - A Free Weighted Histogram.." (J. C

Re: [gmx-users] g_wham missing option

On 2/2/13 12:58 PM, Nash, Anthony wrote: Hi All, I am using Gromacs 4.5.5 and running free energy calculations. According to the article "g_wham - A Free Weighted Histogram.." (J. Chem. Theory. Comput. 2010, 6, 3713-3720), there is the option -bs-method. However, I am unable to find this

[gmx-users] g_wham missing option

Hi All, I am using Gromacs 4.5.5 and running free energy calculations. According to the article "g_wham - A Free Weighted Histogram.." (J. Chem. Theory. Comput. 2010, 6, 3713-3720), there is the option -bs-method. However, I am unable to find this option when running g_wham. I want to use b

Re: [gmx-users] g_wham with pull_geometry=position

Hi, thanks for your response, Since I'm using pull_geometry=position I was under the impression that defining pull_dim was not necessary. Instead, I defined pull_vec to specify that the protein should be pulled along <0 0 1> I was previously using pull_geometry=distance with pull_dim= N N Y but fo

Re: [gmx-users] g_wham with pull_geometry=position

Hi, are you sure that you want to have pull_dim = Y Y Y (which is the default)? When you want to pull only in z direction, I would use pull_dim = N N Y. Otherwise, your z coordinate is not your reaction coordinate. If you want to pull in 3 dimensions you probably want to use pull_geomery=di

[gmx-users] g_wham with pull_geometry=position

Hello all, My simulation involves the pulling of a protein in the negative direction of the z-axis into a stationary hydrophobic self-assembled monolayer surface model (MTHL) using the position pull geometry. My umbrella parameters in the md_umbrella.mdp file are as follows: pull= umb

Re: [gmx-users] g_wham problem with negative COM differences

Anni Kauko wrote: Anni Kauko wrote: > > > > Date: Wed, 11 Apr 2012 08:38:05 -0400 > > From: "Justin A. Lemkul" mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> > > Subje

Re: [gmx-users] g_wham problem with negative COM differences

> Anni Kauko wrote: > > > > > > Date: Wed, 11 Apr 2012 08:38:05 -0400 > > > From: "Justin A. Lemkul" mailto:jalem...@vt.edu > >> > > > Subject: Re: [gmx-users] g_wham problem with negative COM > differences > > >

[gmx-users] g_wham problem with negative COM differences

38:05 -0400 > From: "Justin A. Lemkul" mailto:jalem...@vt.edu>> > Subject: Re: [gmx-users] g_wham problem with negative COM differences > To: Discussion list for GROMACS users <mailto:gmx-users@gromacs.org>> > Message-ID: <4f857b2d.3050...@vt.ed

Re: [gmx-users] g_wham problem with negative COM differences

Anni Kauko wrote: Date: Wed, 11 Apr 2012 08:38:05 -0400 From: "Justin A. Lemkul" mailto:jalem...@vt.edu>> Subject: Re: [gmx-users] g_wham problem with negative COM differences To: Discussion list for GROMACS users mailto:gmx-users@gromacs.org>> Mess

Re: Re: [gmx-users] g_wham problem with negative COM differences

> Date: Wed, 11 Apr 2012 08:38:05 -0400 > From: "Justin A. Lemkul" > Subject: Re: [gmx-users] g_wham problem with negative COM differences > To: Discussion list for GROMACS users > Message-ID: <4f857b2d.3050...@vt.edu> > Content-Type: text/plain; charset=ISO-

Re: [gmx-users] g_wham problem with negative COM differences

Anni Kauko wrote: Hi! I try to perform pmf calculations for case where a peptide shifts through the membrane. My COM differences should vary from 2.3 to -2.5. My problem is that g_wham plots negative COM difference as they would be positive. In pullx-files the COM differences are treated

[gmx-users] g_wham problem with negative COM differences

Hi! I try to perform pmf calculations for case where a peptide shifts through the membrane. My COM differences should vary from 2.3 to -2.5. My problem is that g_wham plots negative COM difference as they would be positive. In pullx-files the COM differences are treated correctly (look below). M

Re: [gmx-users] g_wham position 0

Hi, the key Umb. Pos. 0.0 indicates the the umbrella center of this simulaiton is at 0.0, not that the profile should starts at zero. Beginning and end of profile are set with -min -max. cheers, Jochen Am 3/22/12 7:03 PM, schrieb rainy908: Hi all, I am experiencing a potential problem wi

[gmx-users] g_wham position 0

Hi all, I am experiencing a potential problem with my PMF curve not starting at position 0 of the reaction coordinate, which is defined by a path starting from 0.0 nm and ending at 0.5 nm. When I run the GROMACS g_wham analysis at Umb. Pos 0.0 (see below), to say, 0.02 nm, the PMF curve doesn't s

Re: [gmx-users] g_wham with cylinder geometry

Hi MPID, I just stepped over your message quite late, so sorry for the late reply. You can simply generate a new set of tpr files with pull_dim= N N Y, and use that one in g_wham. g_wham only picks the force constants and umbrella centers from the tpr files, so you are fine with that. Jochen

[gmx-users] g_wham with cylinder geometry

Hi everyone. I ran an umbrella sampling simulation of a protein in a membrane. I used pull_geometry=cylinder. I tried to analyze the results with g_wham. I got this error: Fatal error: With pull geometry 'cylinder', expected pulling in Z direction only. However, found dimensions [Y Y Y] The manu

Re: [gmx-users] g_wham error

rajat desikan wrote: Sorry, sorry...I have used Opls AA. The methane was going back and forth in the pulling during which I generated the configurations. Assuming you used a harmonic potential, that is to be expected. As long as you have set up reasonable spacing for your sampling windows

Re: [gmx-users] g_wham error

rajat desikan wrote: Yeah, I have partial charges on, -0.24 on carbon and + 0.06 on the hydrogens...I am using Gromos 96 53a6 force field. I am getting a couple This is fundamentally incorrect. 53A6 is a united-atom force field, so each methane should be a single particle with 0 charge usi

Re: [gmx-users] g_wham error

Yeah, I have partial charges on, -0.24 on carbon and + 0.06 on the hydrogens...I am using Gromos 96 53a6 force field. I am getting a couple of doubts Justin. Since, I am pulling the methane away steadily, it should smoothly increase the distance right? But the second methane molecule is both increa

Re: [gmx-users] g_wham error

rajat desikan wrote: Justin, Should i turn off charges on the methane molecules? I have left them on. What force field are you using? If you've got an all-atom model of methane, you should have partial charges. -Justin On Mon, Nov 21, 2011 at 12:32 AM, Justin A. Lemkul

Re: [gmx-users] g_wham error

Justin, Should i turn off charges on the methane molecules? I have left them on. On Mon, Nov 21, 2011 at 12:32 AM, Justin A. Lemkul wrote: > > > rajat desikan wrote: > >> My simulations are for 10 ns in each window. There is a lot of noise in >> my wham too. I am enclosing my wham for pullf (the

Re: [gmx-users] g_wham error

rajat desikan wrote: My simulations are for 10 ns in each window. There is a lot of noise in my wham too. I am enclosing my wham for pullf (the earlier was pullx) and pmf. They are really looking strange. Stronger restraint means force constant? >From literature, I kept it at 3000. Those

Re: [gmx-users] g_wham error

rajat desikan wrote: hi Justin I am not able to tell where the lack of overlap is. This is the first wham plot I am looking at. In your tutorial and literature, the wham plots are so clear. Can you please help me? Thanks. It looks like your first one or two windows were not restrained suf

Re: [gmx-users] g_wham error

Oh lovely...thanks for the quick reply Justin :)... On Sat, Nov 19, 2011 at 10:57 PM, Justin A. Lemkul wrote: > > > rajat desikan wrote: > >> Hi >> I am a new gromacs user. I just completed Justin's umbrella sampling >> tutorial. I am doing a PMF calculation between 2 methane molecules in >> wat

Re: [gmx-users] g_wham error

rajat desikan wrote: Hi I am a new gromacs user. I just completed Justin's umbrella sampling tutorial. I am doing a PMF calculation between 2 methane molecules in water. The simulation has run fine till the g_wham step. My command is -- g_wham -it tpr-files.dat -if pullf-files.dat -o -hist

[gmx-users] g_wham error

Hi I am a new gromacs user. I just completed Justin's umbrella sampling tutorial. I am doing a PMF calculation between 2 methane molecules in water. The simulation has run fine till the g_wham step. My command is -- g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 2000 I get a

Re: [gmx-users] g_wham and entropic subtraction

On 2011-11-11 21:29, Sanku M wrote: Hi, I just wanted to check whether g_wham ( in gromacs4.5.4) already subtractthe entropic contribution ( -2KTlog(r) term ) term when unbiasing the histogram obtained from umbrella sampling using distance in 3D as a reaction coordinate. Thanks Sanku If it does

[gmx-users] g_wham and entropic subtraction

Hi,   I just wanted to check whether g_wham ( in gromacs4.5.4) already subtract the entropic contribution ( -2KTlog(r) term ) term when unbiasing the histogram obtained from umbrella sampling using distance in 3D as a reaction coordinate. Thanks Sanku-- gmx-users mailing listgmx-users@gromac

[gmx-users] g_wham issue

Please provide very much more information. Unless somebody has run into the exact thing that you are describing it is currently impossible for us to help you. One thing I can suggest now is to construct histograms of the sampling from the coord.xvg files yourself with some scripting and plo

[gmx-users] g_wham issue

Hi all: I have been trying to figure out a problem in our umbrella sampling simulation. We are simulating a coarse grained protein passing through a coarse grained lipid bilayer. In the pull simulation, the protein was made to move from +z=6 nm of the box through the lipid layer at z=0 to z= -

[gmx-users] g_wham PMF profile

Dear all, thanks a lot for your suggestions that give me the possibility to improve my calculation. All the best Anna -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_List

Re: [gmx-users] g_wham PMF profile

The reliability of the PMF curve depends on the reliability of sampling. If you're over-sampling in some regions along the reaction coordinate and under-sampling in others, then the weighting is probably wrong and the result inaccurate. I can't tell exactly from your description what's go

[gmx-users] g_wham PMF profile

There is no such thing as over-sampling. There is no problem induced by having more sampling in one region except in relation to the fact that you now have less sampling in some other region. That is to say, if you have a totally converged PMF and then sample the first half of the umbrellas

Re: [gmx-users] g_wham PMF profile

On 2011-03-13 15.15, anna wrote: Thank you! and, is there a problem if I'm over-sampling some regions in the case where in the other regions I have got a good (not a under-one) sampling? This over-sampled region can invalidate my DeltaG value? best, Anna Check our recent paper Jochen S.

[gmx-users] g_wham PMF profile

Thank you! and, is there a problem if I'm over-sampling some regions in the case where in the other regions I have got a good (not a under-one) sampling? This over-sampled region can invalidate my DeltaG value? best, Anna -- gmx-users mailing listgmx-users@gromacs.org http://lists.gro

Re: [gmx-users] g_wham PMF profile

battis...@libero.it wrote: Dear all I'd like to get the PMF using g_wham after umbrella sampling. I saw that PMF profile dipend very strong from the windows selected in the z (reaction coordinate) direction. My idea is that the result of this method is much more qualitative than quantitativ

[gmx-users] g_wham PMF profile

Dear all I'd like to get the PMF using g_wham after umbrella sampling. I saw that PMF profile dipend very strong from the windows selected in the z (reaction coordinate) direction. My idea is that the result of this method is much more qualitative than quantitative. Are you in agreement with me

Re: [gmx-users] g_wham

Nilesh Dhumal wrote: Hello I am trying run g_wham for umbrella sampling. Before going for sampling I want to plot PMF. I have one .tpr file and one one pullf.xvg. How can I use them to run P You can't. Umbrella sampling implies that you've done simulations in multiple sampling windows al

[gmx-users] g_wham

Hello I am trying run g_wham for umbrella sampling. Before going for sampling I want to plot PMF. I have one .tpr file and one one pullf.xvg. How can I use them to run P Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search

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

On 9/18/10 Sep 18,10:17 PM, Jochen Hub wrote: On 9/10/10 Sep 10,2:40 PM, Eudes Fileti wrote: 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. ---

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

On 9/10/10 Sep 10,2:40 PM, Eudes Fileti wrote: 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 c

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

Eudes Fileti wrote: 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, li

[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: Pul

[gmx-users] g_wham

Thanks Justin Is it possible to use g_wham with pull_geometry = direction, I read on the website that you couldn't but was wondering if this had changed? Gavin Justin A. Lemkul wrote: > > > Gavin Melaugh wrote: >> Hi All >> >> I am using COM pulling to pull two molecules together in order to >>

Re: [gmx-users] g_wham gets stuck

Amir Marcovitz wrote: Thank you Jochem, In your last reply, did you mean that i can perform the WHAM on Various histograms that were collected with different force constants? i mean , will it know to do the correction for the biasing potential Yes, WHAM does not require identical force consta

Re: [gmx-users] g_wham gets stuck

Thank you Jochem, In your last reply, did you mean that i can perform the WHAM on Various histograms that were collected with different force constants? i mean , will it know to do the correction for the biasing potential amir On Fri, Apr 30, 2010 at 4:00 PM, Jochen Hub wrote: > Justin A. Lemkul

Re: [gmx-users] g_wham gets stuck

Justin A. Lemkul wrote: Amir Marcovitz wrote: Thanks for your answers, I tried to struggle a bit more with that today. my input dat files listings (i.e., tpr-files.dat, pullf-files.dat and pullx-files.dat) are fine and consistent with other in terms of file numbering. i use gromacs 4.0.5 o

Re: [gmx-users] g_wham gets stuck

Amir Marcovitz wrote: Thanks for your answers, I tried to struggle a bit more with that today. my input dat files listings (i.e., tpr-files.dat, pullf-files.dat and pullx-files.dat) are fine and consistent with other in terms of file numbering. i use gromacs 4.0.5 on Linux with gcc 4.1.2

Re: [gmx-users] g_wham gets stuck

Thanks for your answers, I tried to struggle a bit more with that today. my input dat files listings (i.e., tpr-files.dat, pullf-files.dat and pullx-files.dat) are fine and consistent with other in terms of file numbering. i use gromacs 4.0.5 on Linux with gcc 4.1.2 compiler. i run: *g_wham -it

Re: [gmx-users] g_wham gets stuck

Amir Marcovitz wrote: Hi All, I have some problems with g_wham, and i already gone through all the postings and didn't find a hint.. basically, I'm trying to calculate PMF between two charged plates. I've performed a pulling simulation between the 2 plates according to Justin's UMBRELLA tut

Re: [gmx-users] g_wham gets stuck

Amir Marcovitz wrote: Hi All, I have some problems with g_wham, and i already gone through all the postings and didn't find a hint.. For problems like these (which are hard to diagnose!), your Gromacs version, compilers used, OS, etc. would be useful. basically, I'm trying to calculate

[gmx-users] g_wham gets stuck

Hi All, I have some problems with g_wham, and i already gone through all the postings and didn't find a hint.. basically, I'm trying to calculate PMF between two charged plates. I've performed a pulling simulation between the 2 plates according to Justin's UMBRELLA tutorial in the website (all st

Re: [gmx-users] g_wham giving flat free energy

Michael McGovern wrote: Hi everyone. I'm having some trouble using g_wham to analyze some results. I have some simulations from gromacs 3.3 using the pull code. I'm using the latest version of g_wham to analyze the results, which the help file says is ok, using the -ip option. I've gotten

[gmx-users] g_wham giving flat free energy

Hi everyone.  I'm having some trouble using g_wham to analyze some results.  I have some simulations from gromacs 3.3 using the pull code.  I'm using the latest version of g_wham to analyze the results, which the help file says is ok, using the -ip option.   I've gotten almost everything to work

Re: [gmx-users] g_wham error

g_wham -ix PREPxvg.dat -it PREPtpr.dat The -ix option expects the pull positions. If you want to provide the pull forces to g_wham, use the -if option. Cheers, Jochen PREPxvg.dat and PREPtpr.dat are lists of the respective xvg and tpr files. They are both in the same order, although

Re: [gmx-users] g_wham error

Justin A. Lemkul wrote: Gard Nelson wrote: Here's my .xvg: # This file was created Mon Mar 8 01:50:07 2010 # by the following command: # /opt/apps/intel10_1/mvapich1_1_0_1/gromacs/4.0.5/bin/mdrun_mpi -multi 31 -deffnm onePREP -px onePREP -np 2976 -maxh 3 Note, too, that this command doe

Re: [gmx-users] g_wham error

Gard Nelson wrote: Here's my .xvg: # This file was created Mon Mar 8 01:50:07 2010 # by the following command: # /opt/apps/intel10_1/mvapich1_1_0_1/gromacs/4.0.5/bin/mdrun_mpi -multi 31 -deffnm onePREP -px onePREP -np 2976 -maxh 3 # # /opt/apps/intel10_1/mvapich1_1_0_1/gromacs/4.0.5/bin/mdr

[gmx-users] g_wham error

Here's my .xvg: # This file was created Mon Mar 8 01:50:07 2010 # by the following command: # /opt/apps/intel10_1/mvapich1_1_0_1/gromacs/4.0.5/bin/mdrun_mpi -multi 31 -deffnm onePREP -px onePREP -np 2976 -maxh 3 # # /opt/apps/intel10_1/mvapich1_1_0_1/gromacs/4.0.5/bin/mdrun_mpi is part of G R O M

Re: [gmx-users] g_wham error

Gard Nelson wrote: Hi all, I'm trying to analyze a series of umbrella sampling windows, but I get the following error: Program g_wham, VERSION 4.0.7 Source code file: gmx_wham.c, line: 1397 Fatal error: Found 1 pull groups in onePREP0.tpr, but 1 data columns in onePREP0.xvg (expected 6) m

[gmx-users] g_wham error

Hi all, I'm trying to analyze a series of umbrella sampling windows, but I get the following error: Program g_wham, VERSION 4.0.7 Source code file: gmx_wham.c, line: 1397 Fatal error: Found 1 pull groups in onePREP0.tpr, but 1 data columns in onePREP0.xvg (expected 6) my .mdp file is: title

Re: [gmx-users] g_wham .tpr / .xvg / .dat conversion issues

On 1/6/10 1:51 PM, V Hariharan wrote: Hello All, I am trying to use g_wham to view the PMF for my simulation. I read the g_wham -h help menu, and it requires .dat input files for the -if and -it input options. My output files from mdrun for -s and -pf were .tpr and .xvg files, respectively.

[gmx-users] g_wham .tpr / .xvg / .dat conversion issues

Hello All, I am trying to use g_wham to view the PMF for my simulation. I read the g_wham -h help menu, and it requires .dat input files for the -if and -it input options. My output files from mdrun for -s and -pf were .tpr and .xvg files, respectively. How to I convert my .tpr and .xvg files i

Re: [gmx-users] g_wham error

Ragnarok sdf wrote: While trying to analyse my several windows with g_wham the following error appears : Fatal error: Pull geometry direction not supported The pull geometry "direction" has unfortunatly been forgotten in g_wham by, well, myself (shame on me :-) ). I can add the geometry to

Re: Re: [gmx-users] g_wham error

> > > > > Ragnarok sdf wrote: > > > While trying to analyse my several windows with g_wham the > > following error > > > appears : > > > > > > Fatal error: > > > Pull geometry direction not supported > > > > > > my entry files consist on the several px.xvg

Re: [gmx-users] g_wham error

> > > > Ragnarok sdf wrote: > > > > Ragnarok sdf wrote: > > > While trying to analyse my several windows with g_wham the > > following error > > > appears : > > > > > > Fatal error: > > > Pull geometry direction not supported > > > > > > my entry files con

Re: [gmx-users] g_wham error

Ragnarok sdf wrote: Ragnarok sdf wrote: > While trying to analyse my several windows with g_wham the following error > appears : > > Fatal error: > Pull geometry direction not supported > > my entry files consist on the several px.xvg listed in a .dat

Re: [gmx-users] g_wham error

Ragnarok sdf wrote: While trying to analyse my several windows with g_wham the following error appears : Fatal error: Pull geometry direction not supported my entry files consist on the several px.xvg listed in a .dat entry file and the several .tpr from each of the simulations also listed in

[gmx-users] g_wham error

While trying to analyse my several windows with g_wham the following error appears : Fatal error: Pull geometry direction not supported my entry files consist on the several px.xvg listed in a .dat entry file and the several .tpr from each of the simulations also listed in a tpr.dat file_

Re: [gmx-users] g_wham problem

Oh, that would be convenient.   Thanks.   --- 09年8月3日，周一, Justin A. Lemkul 写道： 发件人: Justin A. Lemkul 主题: Re: [gmx-users] g_wham problem 收件人: "Discussion list for GROMACS users" 日期: 2009年8月3日,周一,上午9:01 accomp lin wrote: >  Dear all >  Gromacs 3.3.3 seems to have a problem

Re: [gmx-users] g_wham problem

accomp lin wrote: Dear all Gromacs 3.3.3 seems to have a problem with g_wham and there is a fixed version from David Bostick of Scripps. So, does anybody has this fixed version of g_wham or is there anybody know that where I can find it? My email address is " accomp...@student.dlut.edu.c

[gmx-users] g_wham problem

  Dear all   Gromacs 3.3.3 seems to have a problem with g_wham and there is a fixed version from David Bostick of Scripps. So, does anybody has this fixed version of g_wham or is there anybody know that where I can find it?   My email address is " accomp...@student.dlut.edu.cn "   Thanks a lot J

Re: [gmx-users] g_wham error

mirc...@sjtu.edu.cn wrote: > gunzip: stdin: not in gzip format > > --- > Program g_wham, VERSION 3.3.3 > Source code file: gmx_wham.c, line: 89 > > Fatal error: > This does not appear to be a valid pdo file > ---

[gmx-users] g_wham error

Dear All: I did some umbrella sampling and got series of .pdo files. I want to calculate potential of mean force (PMF) by g_wham command. However I encount some problems: when I input the following command: g_wham pull.pdo -o xx.xvg -hist xx2.xvg

[gmx-users] g_wham output

Dear all, I have used the PULL code in gmx 4 to unwind part of my protein. 10 runs were performed (all pulling the pulled group from 1.3 nm to 4.3 nm away from the reference). The output seems ok from the pullx.xvg and the trajectories. However, when using g_wham to obtain the PMF there seems t

Re: [gmx-users] g_wham 4..0.x input file: tpr-files.dat ?

Y.C. Huang wrote: Hello everyone: I have a question about the g_wham version 4.0.x. After I tried to do umbrella sampling by using mdrun 4.0.x, I had these files: pullf.xvg pullx.xvg umbrella_test.err umbrella_test.tpr umbrella_test.gro umbrella_test.trr umbrella_test.edr umbrella_test.log um

[gmx-users] g_wham 4..0.x input file: tpr-files.dat ?

Hello everyone: I have a question about the g_wham version 4.0.x. After I tried to do umbrella sampling by using mdrun 4.0.x, I had these files: pullf.xvg pullx.xvg umbrella_test.err umbrella_test.tpr umbrella_test.gro umbrella_test.trr umbrella_test.edr umbrella_test.log umbrella_test_prev.cpt u

Re: [gmx-users] g_wham Error bars

Raphael Alhadeff wrote: > Hello everyone, > > I wanted to ask if anyone knows how to compute standard deviation, for the > sake of adding error bars to an energy profile output using g_wham (PMF using > umbrella sampling in my case). > > Just to clarify, I am talking about the deviation of the

[gmx-users] g_wham Error bars

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

Re: [gmx-users] g_wham Error bars

Hello, As far as I know, it is not possible to directly calculate and error bar with g_wham . At that point, you've got several options: 1) You can run several times your umbrella sampling simulations, calculate several PMFs, then calculate an average and a standard deviation 2) i

[gmx-users] g_wham Error bars

Hello everyone, I wanted to ask if anyone knows how to compute standard deviation, for the sake of adding error bars to an energy profile output using g_wham (PMF using umbrella sampling in my case). Just to clarify, I am talking about the deviation of the energy profile on ONE simulation (com

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