[gmx-users] ngmx
Hello! Why does the animation with ngmx not work always properly? How can I save the animation in Linux? Thanks! Thomas -- 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_Lists/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/Support/Mailing_Lists
[gmx-users] viscosity
Hello, I calculate the viscosity with g_energy using option -vis (Gromacs 4.0.7): g_energy -f file.trr -s file.tpr -vis visc.xvg Why do I get viscosity values only until the half of the simulation time? Thomas -- 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_Lists/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/Support/Mailing_Lists
[gmx-users] Viscosity and surface tension
Hello, I want to calculate bulk viscosity and surface tension. Gromacs 4.0.7 provides options in g_energy: 1) Do I need long simulations to get a constant value for the bulk viscosity using -vis option? 2) How is the surface tension (#Surf*SurfTen) calculated? Regards, Thomas -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de -- 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_Lists/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/Support/Mailing_Lists
[gmx-users] g_energy
Hello, the g_energy tool in Gromacs 4.0.7 provides calculation of viscosity (-vis) and surface tension (-o surften): a) Both, the shear and bulk viscosity are calculated with -vis tool. What are the equations for calculating them? In the manual, there is only the equation for the shear viscosity. Are these values reliable? b) How is the surface tension calculated, is it also a reliable method? Regards, Thomas-- 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_Lists/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/Support/Mailing_Lists
[gmx-users] Fw: g_energy
Short reminder. I am lloking forward to your answer. Thomas From: Thomas Koller Sent: Monday, May 16, 2011 11:37 PM To: gmx-users@gromacs.org Subject: g_energy Hello, the g_energy tool in Gromacs 4.0.7 provides calculation of viscosity (-vis) and surface tension (-o surften): a) Both, the shear and bulk viscosity are calculated with -vis tool. What are the equations for calculating them? In the manual, there is only the equation for the shear viscosity. Are these values reliable? b) How is the surface tension calculated, is it also a reliable method? Regards, Thomas-- 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_Lists/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/Support/Mailing_Lists
[gmx-users] g_energy
Hello, the g_energy tool in Gromacs 4.0.7 provides calculation of viscosity (-vis) and surface tension (-o surften): a) Both, the shear and bulk viscosity are calculated with -vis tool. What are the equations for calculating them? In the manual, there is only the equation for the shear viscosity. Are these values reliable? b) How is the surface tension calculated, is it also a reliable method? Regards, Thomas-- 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_Lists/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/Support/Mailing_Lists
[gmx-users] Re: gmx-users Digest, Vol 83, Issue 123
I managed it now. Thanks for all your help. Thomas Original-Nachricht > Datum: Thu, 17 Mar 2011 14:26:46 +0100 (CET) > Von: gmx-users-requ...@gromacs.org > An: gmx-users@gromacs.org > Betreff: gmx-users Digest, Vol 83, Issue 123 > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@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. installation of gromacs (Thomas Koller) >2. Re: installation of gromacs (Mark Abraham) >3. Re: installation of gromacs (Diego Enry) >4. Re: installation of gromacs (Justin A. Lemkul) >5. Re: installation of gromacs (Mark Abraham) > > > ------ > > Message: 1 > Date: Thu, 17 Mar 2011 12:24:46 +0100 > From: "Thomas Koller" > Subject: [gmx-users] installation of gromacs > To: gmx-users@gromacs.org > Message-ID: <20110317112446.249...@gmx.net> > Content-Type: text/plain; charset="utf-8" > > Now I get this again: > > checking for fftw3.h... configure: error: Cannot find the default external > FFT library (fftw3). > > Please follow my way: > > i) I unpacke fftw and gromacs to two folders. > iii) I go the the fftw folder and make: > - ./configure --prefix=$HOME/local/fftw3 --enable-sse --enable-shared > --enable-float > - make -j > - make install > - export CPPFLAGS="-I/home/local/fftw/include" > - export LDFLAGS="-L/home/local/fftw/lib" > > iii) Then I go (cd) to the folder gromacs-4.0.7 > - ./configure --prefix=$HOME/local/gromacs > - Now I get the error writen above. > > Is my way wrong, do I have to insert the fftw folder into the gromacs > folder, is the sequence wrong? > > I wish I can have access soon. :( > > Thomas > > -- > Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir > belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de > > > -- > > Message: 2 > Date: Thu, 17 Mar 2011 22:28:33 +1100 > From: Mark Abraham > Subject: Re: [gmx-users] installation of gromacs > To: Discussion list for GROMACS users > Message-ID: <7640bbf378.4d828...@anu.edu.au> > Content-Type: text/plain; charset="iso-8859-1" > > > > On 17/03/11, Thomas Koller wrote: > > Now I get this again: > > > > checking for fftw3.h... configure: error: Cannot find the default > external FFT library (fftw3). > > > > > > > > > Please follow my way: > > > > i) I unpacke fftw and gromacs to two folders. > > iii) I go the the fftw folder and make: > > - ./configure --prefix=$HOME/local/fftw3 --enable-sse > --enable-shared --enable-float > > > > You've installed in /home/local/fftw3... > > > > > - make -j > > - make install > > - export CPPFLAGS="-I/home/local/fftw/include" > > - export LDFLAGS="-L/home/local/fftw/lib" > > > > ... but told configure later to look in /home/local/fftw > > That doesn't work. > > Even when it does, it's likely that you'll still need to look at the last > few hundred lines of config.log to actually diagnose the problem... > > Mark > > > > > > > iii) Then I go (cd) to the folder gromacs-4.0.7 > > - ./configure --prefix=$HOME/local/gromacs > > - Now I get the error writen above. > > > > Is my way wrong, do I have to insert the fftw folder into the gromacs > folder, is the sequence wrong? > > > > I wish I can have access soon. :( > > > > Thomas > > > > -- > > Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir > > belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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
[gmx-users] installation of gromacs
Now I get this again: checking for fftw3.h... configure: error: Cannot find the default external FFT library (fftw3). Please follow my way: i) I unpacke fftw and gromacs to two folders. iii) I go the the fftw folder and make: - ./configure --prefix=$HOME/local/fftw3 --enable-sse --enable-shared --enable-float - make -j - make install - export CPPFLAGS="-I/home/local/fftw/include" - export LDFLAGS="-L/home/local/fftw/lib" iii) Then I go (cd) to the folder gromacs-4.0.7 - ./configure --prefix=$HOME/local/gromacs - Now I get the error writen above. Is my way wrong, do I have to insert the fftw folder into the gromacs folder, is the sequence wrong? I wish I can have access soon. :( Thomas -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de -- 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_Lists/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/Support/Mailing_Lists
[gmx-users] installation of gromacs
Hi Nuno, I have still problems with the insatllation of the 4.0.7 version. After unpacking of fftw and gromacs, I did: In the fftw folder: ./configure --prefix=$HOME/local/fftw3 --enable-sse --enable-shared --enable-float make -j make install export CPPFLAGS="-I$HOME/local/fftw3/include" export LDFLAGS="-L$HOME/local/fftw3/lib" In the gromacs-4.0.7 folder: ./configure --prefix=$HOME/local/gromacs --enable-shared At the end I get: checking for void*... yes checking size of void*... configure: error: cannot compute sizeof (void*) What does that mean? Why is this not working? Regards, Thomas -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de -- 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_Lists/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/Support/Mailing_Lists
[gmx-users] installation of gromacs
Hello, I did the procedure as described, but at the end of the configuration of gromacs, I obtain this message: checking size of void*... configure: error: cannot compute sizeof (void*) See `config.log' for more details. What is the problem? Regards, Thomas -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de -- 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_Lists/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/Support/Mailing_Lists
[gmx-users] Re: installation of gromacs (Dommert Florian)
Hello, I have installed Gromacs but if I want to open another terminal and run another simulation it does not work. Do I need a further step? Regards, Thomas -- GMX DSL Doppel-Flat ab 19,99 Euro/mtl.! Jetzt mit gratis Handy-Flat! http://portal.gmx.net/de/go/dsl -- 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_Lists/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/Support/Mailing_Lists
[gmx-users] Re: installation of gromacs (Dommert Florian)
Hello, I have followed you instructions and it was working: GROMACS is installed under /home/thomas/local/gromacs. I wanted to run a simulation in this folder but I get the error: ./run0_NVT.sh: line 2: grompp: command not found nohup: appending output to `nohup.out' nohup: cannot run command `mdrun': No such file or directory Do I need further steps after the installation? Regards, Thomas -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de -- 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_Lists/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/Support/Mailing_Lists
[gmx-users] installation of gromacs
Hello, I want to install Gromacs 4.5.3 in my computer. Therefore I downloaded fftw 3.2.2 and did as in the instructions: ./configure --enable-float make make install After that I ran: ./configure with Gromacs, but I always get: checking for fftw3.h... configure: error: Cannot find the default external FFT library (fftw3). Other alternatives are 'fftw2', or 'mkl' for Intel MKL. You are STRONGLY recommended to use one of these - fftw is free. make is not working after this: make: *** No targets specified and no makefile found. Stop. What is going wrong? Thomas -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de -- 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_Lists/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/Support/Mailing_Lists
[gmx-users] RE: heat capacity etc. (Thomas Koller)
I dont know exactly what you mean. Here you can see my output data: Energy AverageRMSDFluct. Drift Tot-Drift --- Potential -48.8499 1.82144 1.81841 -0.00781553 -0.3638 Kinetic En.50.7548 1.42996 1.42991 -0.000872827 -0.0406286 Total Energy 1.90489 2.32653 2.3236 -0.00868836 -0.404429 Temperature298.15 8.40003 8.39975 -8.84014e-05 -0.238666 Pressure (bar) 1.66395 713.24 713.236 0.00302056 8.15491 Volume 21.0391 0.179301 0.178412-2.2873e-05 -0.0617527 pV-0.45227 903.541 903.536 0.00377916 10.203 Heat Capacity Cv: 13.3969 J/mol K (factor = 0.0460384) Isothermal Compressibility: 3.71208e-05 /bar Adiabatic bulk modulus:26939.1 bar i) How should I calculate the isobaric heat capacity with this values, bu udage of the Fluct. in the 3rd column? ii) How is the isothermal compressibility here calculated? Regards, Thomas -- Schon gehört? GMX hat einen genialen Phishing-Filter in die Toolbar eingebaut! http://www.gmx.net/de/go/toolbar -- 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_Lists/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/Support/Mailing_Lists
[gmx-users] RE: heat capacity etc. (Thomas Koller)
Thanks, the equation for the heat capacity is: c(P) = delta(H(average))/delta(T(average)) So do it have to take the fluctuations (which are listed with g_energy) of U(tot) and pV as well as of T to calculate c(P)? The problem is the delta. The same is with the thermal compressibility: a(P) = 1/V(average) * delta(V(average))/delta(T(average)) Another question: Why should I take U(tot) and not only the potential for c(P)? The same is for the heat of vaporization, here also with U(tot)? Regards, Thomas -- NEU: FreePhone - kostenlos mobil telefonieren und surfen! Jetzt informieren: http://www.gmx.net/de/go/freephone -- 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_Lists/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/Support/Mailing_Lists
[gmx-users] RE: heat capacity etc.
I have version 4.0.5 and there is no enthalpy in the g_energy tool. Do you see a chance to calculate the isobaric heat capacity as well as the thermal compressibility, which is also not shown? Thomas -- Schon gehört? GMX hat einen genialen Phishing-Filter in die Toolbar eingebaut! http://www.gmx.net/de/go/toolbar -- 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_Lists/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/Support/Mailing_Lists
[gmx-users] Re: heat capacity etc. (David van der Spoel)
You mean that I take the fluctuations of enthalpy (= total energy and PV) and fluctuations of temperature and make simply the ratio to get c(P)? Thomas -- Schon gehört? GMX hat einen genialen Phishing-Filter in die Toolbar eingebaut! http://www.gmx.net/de/go/toolbar -- 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_Lists/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/Support/Mailing_Lists
[gmx-users] heat capacity etc.
Hello, i) I use a NPT ensemble to get the heat capacity c(p). But I always get c(V) when I use option -vis where some properties are listed. What is the standard way to extract the isobaric heat capacity? Which tool should I use? ii) The thermal compressibility is never listed when I use g_energy. I use a NPT ensemble, same as in i). How can I get the thermal compressibility with g_energy exactly? Regards, Thomas -- Schon gehört? GMX hat einen genialen Phishing-Filter in die Toolbar eingebaut! http://www.gmx.net/de/go/toolbar -- 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_Lists/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/Support/Mailing_Lists
[gmx-users] RE: heat capacity etc.
Hello, i) I use a NPT ensemble and the tool g_energy to extract the heat capacity. Nose-Hoover thermostat and Parrinello-Rahman barostat are used. Why do I get always c(V)? ii) When I use the tool g_energy -vis, I get the thermal compressibility, the adiabatic bulk modulus, but not the thermal expansion coefficient. How can I get this? Thomas -- GMX DSL Doppel-Flat ab 19,99 Euro/mtl.! Jetzt mit gratis Handy-Flat! http://portal.gmx.net/de/go/dsl -- 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_Lists/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/Support/Mailing_Lists
[gmx-users] RE: heat capacity etc.
-- NEU: FreePhone - kostenlos mobil telefonieren und surfen! Jetzt informieren: http://www.gmx.net/de/go/freephone -- 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_Lists/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/Support/Mailing_Lists
[gmx-users] heat capacity etc.
Hello, I want to calculate the isobaric heat capacity, the thermal expansion coefficient and the isothermal compressibility: i) My value for the heat capacity (NPT) is very low. I used option -nmol. Whan can be the reason or is the calculation of this property not accurate with this tool? By the way, why is there always written c(v) although I analyze a NPT run c(P)? ii) How can I obtain the thermal expansion coefficient from the NPT run, I can't see it? The isothermal compressibility is calculated. Regards, Thomas -- GMX DSL Doppel-Flat ab 19,99 Euro/mtl.! Jetzt mit gratis Handy-Flat! http://portal.gmx.net/de/go/dsl -- 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_Lists/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/Support/Mailing_Lists
[gmx-users] excess chemical potential
Hello, I want to calculate the excess chemical potential of one dissolved molecule within an liquid system. The excess chemical potential should be delta G. The equation for delta G is given in manual: With -fee an estimate is calculated for the free-energy difference with an ideal gas state: Delta G = G(N,p,T) - G idgas(N,p,T) = kT ln < e(Upot/kT) > What is the meaning of this Upot? Does it describe the interaction energy of the dissolved gas what I need for the calculations. Or do I need the two values for delta G with 1 molecule gas and without it to calculate the Henry constant with delta G? Regards, Thomas -- NEU: FreePhone - kostenlos mobil telefonieren und surfen! Jetzt informieren: http://www.gmx.net/de/go/freephone -- 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_Lists/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/Support/Mailing_Lists
[gmx-users] henry constant
Hello, I want to calculate the henry constant for a soluble gas in a solvent. For that, I use the tool -fee in g_energy to get deltaG. Is that the excess chemical potential, with which I can calculate the henry constant? Or is it not possible to calculate the henry-constant with this tool? Regards, Thomas -- NEU: FreePhone - kostenlos mobil telefonieren und surfen! Jetzt informieren: http://www.gmx.net/de/go/freephone -- 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_Lists/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/Support/Mailing_Lists
[gmx-users] henry constant
Hello, I want to calculate the henry constant for a soluble gas in a solvent. For that, I use the tool -fee in g_energy to get deltaG. Is that the excess chemical potential, with which I can claculate the henry constant? Regards, Thomas -- NEU: FreePhone - kostenlos mobil telefonieren und surfen! Jetzt informieren: http://www.gmx.net/de/go/freephone -- 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_Lists/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/Support/Mailing_Lists
[gmx-users] widom insertion
Hello, is Widom test particle insertion and with that, the calculation of solubility in Gromacs possible? Regards, Thomas -- Schon gehört? GMX hat einen genialen Phishing-Filter in die Toolbar eingebaut! http://www.gmx.net/de/go/toolbar -- 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_Lists/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/Support/Mailing_Lists
[gmx-users] diffusion coefficients
Hello, I'm investigating the diffusion coefficient of gases in liquids. Therefore, I insert some molecules with the genbox tool in an equilibrated system. After a NPT run to adjust the density, I'm running an NVT simulation to calculate the diffusion coefficient (g_msd). MSD of the liquids are quite linear, but the gas MSDs show sometime fluctuations, even with negative slopes within the run. What can be the problem or is this strategy right? Regards, Thomas -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de -- 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_Lists/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/Support/Mailing_Lists
[gmx-users] NVE simulation
Hello! Is it possible to run NVE simulations insteed of NVT or NPT in Gromacs? Thomas -- Schon gehört? GMX hat einen genialen Phishing-Filter in die Toolbar eingebaut! http://www.gmx.net/de/go/toolbar -- 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_Lists/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/Support/Mailing_Lists
[gmx-users] NVT run
Hello, I calculate the density of my lquid in the equilibrated time range of the density-time plots (NPT runs). I use the gro file of these NPT runs for NVT runs to calculate the self diffusion coefficient at the simulated density. Concerning this gro file: Is this taken from the end of the NPT run or the average of the equilibrated time range? Because this is important for the following NVT simulation. Which system size is listed there at the bottom of the output gro file? Regards, Thomas -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de -- 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_Lists/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/Support/Mailing_Lists
[gmx-users] Improper dihedral
Hello! I want to use improper type 4 in the top file, but this is not working. When I switch to type 2 everything is fine. What is the problem with type 4? Regards, Thomas -- Neu: GMX De-Mail - Einfach wie E-Mail, sicher wie ein Brief! Jetzt De-Mail-Adresse reservieren: http://portal.gmx.net/de/go/demail -- 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_Lists/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/Support/Mailing_Lists
[gmx-users] Questions concerning autocorrealtion function
Hello! i)Here are the commands for my problem with the autocorrelation function which I mentioned in mails before: g_dist -f traj.trr -s topol.tpr -n index.ndx -o dist.xvg g_analyze -f dist.xvg -ac autocorr.xvg -P 2 Fatal error: Incompatible mode bits: normal and vector (or Legendre) What is the problem here? ii) Usually the rdfs are calculated until half the box length. How can I increase the distance range? Regards, Thomas -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de -- 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_Lists/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/Support/Mailing_Lists
[gmx-users] rdf range
Hello! One question: I want to plot the rdf functions. How can I adjust to fix how far the rdf is plotted over the distance? I want to see the rdfs over long distance r. Where can I adjust that? Thanks! Thomas -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de -- 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_Lists/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/Support/Mailing_Lists
[gmx-users] Re: gmx-users Digest, Vol 81, Issue 204
Hello! Due to the fact that I still got no reply I ask you once more: i) I studied the topic of autocorrelation function in Gromacs. For instance, I can define any distance between different atoms of my molecule over time (g_dist) as *.xvg file. For g_analyze, I use this as input and plot the autocorrelation function (-av) and can fit it with -fitfn exp. But when I want to use the Legendre option -P 2 to get a second order legendre polynomial (which is used quite often in literature) the error appears: Incompatible mode bits: normal and vector (or Legendre) I think that I need vectors but this can not be done in Gromacs, does it?. How can I get Legendre functions, also for dihedrals? ii) I use bond type 1 (harmonic bond potential), but I get always linear spiky bond distribution functions, no Gaussian distribution. What is the problem? I'm looking forward to your answers! Thanks. Thomas Original-Nachricht > Datum: Wed, 26 Jan 2011 14:46:57 +0100 (CET) > Von: gmx-users-requ...@gromacs.org > An: gmx-users@gromacs.org > Betreff: gmx-users Digest, Vol 81, Issue 204 > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@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: validation of ligand parametrization (mohsen ramezanpour) >2. decorrelation function (Thomas Koller) >3. Re: Re: segmentation fault while running eneconv (Anna Marabotti) >4. Re: Re: Re: segmentation fault while running eneconv > (Justin A. Lemkul) > > > -- > > Message: 1 > Date: Wed, 26 Jan 2011 16:05:44 +0330 > From: mohsen ramezanpour > Subject: Re: [gmx-users] validation of ligand parametrization > To: Discussion list for GROMACS users > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Dear Dr Mark > Thanks for your guidances. > I am sorry for my last question.My english is not very good,I hope I could > say what was in my mind not what you read :-) > by the way,Thanks for your attention and your reply. > > On Wed, Jan 26, 2011 at 3:55 PM, Mark Abraham > wrote: > > > On 26/01/2011 11:10 PM, mohsen ramezanpour wrote: > > > > Dear Justin > > I don't want to rely on PRODRG server as others. > > I want to do my work as accurate as possible. > > Absolutely I read your papar and I know PRODRG present bad results for > > estimating free energies. > > I want to parametrize my drugs by GROMOS43A1 parameters as you said. > > I know completely how to do it.Thanks for your and other user's > guidances. > > Actually I couldn't find any experimentally data to try to obtain it's > > result.Then i have to > > do what you said.(re-evaluating force field choice and .) > > > > > > Sounds wise. > > > > > > Can you please say me more about this method? > > > > > > It sounds to me like he's said plenty of useful things on the topic :-) > A > > question with a precise focus is much more likely to attract somebody's > > interest. Otherwise, it can sound too much like you're asking for your > work > > to be done for you! > > > > Back on point, if you can't determine a basis for the kind of empiricism > > GROMOS forcefields require, then you may want to choose one of the other > > force fields with a more automated method. That doesn't remove the need > to > > validate, or the conundrum if validation fails, however. It's very easy > to > > do a worthless simulation. Many of them are. Many more of them become so > > because they don't describe enough detail that they could be reproduced. > For > > example, lots of people say just "I used PME with x cutoff" in the same > way > > they did in the 1990s when they used a plain cutoff. I've read three > such in > > the last week. However, that statement is almost useless as an indicator > of > > quality in the electrostatic model. (Oops, I've digressed. Oh well.) > > > > Mark > > > > > > Did you have something like this in your papers? > > Thanks in advance for your reply > > > > On Wed, Jan 26, 2011
[gmx-users] decorrelation function
Hello! I have a question concerning decorrelation/autocorrelation functions: I studied the topic of autocorrelation function in Gromacs. For instance, I can define any distance between different atoms of my IL over time (g_dist) as *.xvg file. For g_analyze, I use this as input and plot the autocorrelation function (-av) and can fit it with -fitfn exp. But when I want to use the Legendre option -P 2 to get a second order legendre polynomial (which is used quite often in literature) the error appears: Incompatible mode bits: normal and vector (or Legendre) I think that I need vectors but this can not be done in Gromacs, does it?. How can I get Legendre functions, also for dihedrals? I'm looking forward to your answer! Thanks. Thomas -- NEU: FreePhone - kostenlos mobil telefonieren und surfen! Jetzt informieren: http://www.gmx.net/de/go/freephone -- 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_Lists/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/Support/Mailing_Lists
[gmx-users] decorrelation function
Hello! I wanted to ask where I can analyze decorrelation functions of, for instance, bonds and torsions? I have the tool g_analyze with option -ac. Here I get negative values, but I thought that the function is in a range between 0 and 1. I would like to have the P2 decorrelation function, so I used -P 2, but it was not working: Fatal error: Incompatible mode bits: normal and vector (or Legendre) Do you know what I must do? Can I also define vectors between different atoms and analyze here the decorrelation function? Regards and thanks, Thomas -- Neu: GMX De-Mail - Einfach wie E-Mail, sicher wie ein Brief! Jetzt De-Mail-Adresse reservieren: http://portal.gmx.net/de/go/demail -- 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_Lists/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/Support/Mailing_Lists
[gmx-users] problem with LINCS
Hello! I have the following problem: I calculated a stable conformation of two ions of an ionic liquid, e.g. the relative positions of both. I used genbox to replicate the pair structure in the simulation box. After that, I started minimization, volume and pressure equilibration. A few steps after the volume equilibration, I got this message: Step 2160, time 4.32 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 2702.127453, max 65115.246094 (between atoms 130 and 131) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 121123 91.90.1378 0.6015 0.1378 130131 90.00.1526 9936.7393 0.1526 ... I use LINCS with h-angles. The whole procedure works when I don't use the conformer pair, but two separate ions inserting randomly in the box. I get no LINCS warning. What can be the problem? Regards and thanks, Thomas -- GMX DSL Doppel-Flat ab 19,99 Euro/mtl.! Jetzt mit gratis Handy-Flat! http://portal.gmx.net/de/go/dsl -- 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_Lists/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/Support/Mailing_Lists
[gmx-users] Question
Hello, running grompp gives me this error: Program grompp, VERSION 4.0.7 Source code file: ../../../../src/kernel/convparm.c, line: 325 Fatal error: unknown function type 20 in ../../../../src/kernel/convparm.c line 326 The two lines 325 and 326 of convparm.c are: break; case F_VSITE2: What can be the error? I never used function type 20. Thanks! Thomas -- GMX DSL Doppel-Flat ab 19,99 Euro/mtl.! Jetzt mit gratis Handy-Flat! http://portal.gmx.net/de/go/dsl -- 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_Lists/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/Support/Mailing_Lists
[gmx-users] Questions concerning Gromacs
Mark, thanks for your reply. The only problem are the improper dihedrals. I show you a example: [ dihedraltypes ] ;improper ftypephik(phi) mult ... A B C D 4 180 5.293 2 Sorry, I use ftype 4, not 2 :) The impropers are listed in the dihedraltypes. The sequence is A B C D where A is the center atom and B, C, D are the surrounding atoms. I think this is right? Later the impropers are specified in the [dihedrals]: [dihedrals] ; i j k lftype ... 1 2 3 4 4 I get the error: ERROR 1 [file binary_ua.top, line 196]: No default Improper Dih. types Fatal error: unknown function type 20 in ../../../../src/kernel/convparm.c line 326 line 326 is: case F_VSITE2: Do you see the error? I don't know what is going wrong. Thanks! Thomas -- GMX DSL Doppel-Flat ab 19,99 Euro/mtl.! Jetzt mit gratis Handy-Flat! http://portal.gmx.net/de/go/dsl -- 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_Lists/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/Support/Mailing_Lists
[gmx-users] Questions concerning Gromacs
Hello, I have some questions concerning the implementation in Gromacs: 1) I want to model a rigid anion of an IL (fixed bonds and angles). The cation is flexible. How can I do that without using constraint types? With LINCS or SHAKE, I can only fix, for instance, bonds with H atoms or all atoms. Can I use high values for the force constants? 2) When implementing improper dihedrals, I write the sequences of the four atoms in the [dihedraltypes] and then fix them in the [dihedral] directive. But I always get the error that the impropers are not defined in the default. What is my problem? I use function type 2. The sequence of impropers is: center atom - neighbor atom - neighbor atom- neighbor atom, as I saw in the manual. 3) For function type 1 of the dihedrals, I implement the equilibrium angle, the force constant and the multiplicity (one value for all kinds). What should I do if I have, for instance, three equilibrium angles, different for the multiplicities (n=1,2,3). How can I implement that in the top file? Thanks for your efforts! Regards, Thomas -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de -- 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_Lists/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/Support/Mailing_Lists
