Re: [gmx-users] question

On 17/11/2010 5:52 PM, Raymond wrote: Why my rdf is larger than 1 in the long range 2010-11-17 Raymond Probably because you did not measure what you thought you measured :-) Mark -- gmx-users mailing listgmx-users@gr

[gmx-users] Reg: pcoupling and ref_p

Hi Gromacians I have created two liquid-liquid interfaces by combining three (DCE-Water-DCE) boxes. I want to calculate the Interfacial surface tension by using the surface tension option in Gromacs. I know that I need to give two values for ref_p one for xy and other for z. it was said in the man

[gmx-users] rdf wrong convergence

I built a system with 2 bulks .left side is liquid side right is gas . But the convergence of the rdf only liquid I calculated is more than 1(about 1.3) . I make a comparison with the Previously work I did (liquid only without gas ) the trend is totally same but the convergence is at 1.3 I don'

Re: Re: [gmx-users] question

I'm very sorry that last Email was just a test ~~~ I don't know how to use this . here is my problem ~~ Thanks very much I built a system with 2 bulks .left side is liquid side right is gas . But the convergence of the rdf only liquid I calculated is more than 1(about 1.3) . I make a comparis

Re: [gmx-users] rdf wrong convergence

On 17/11/2010 8:07 PM, Raymond wrote: I built a system with 2 bulks .left side is liquid side right is gas . But the convergence of the rdf only liquid I calculated is more than 1(about 1.3) . I make a comparison with the Previously work I did (liquid only without gas ) the trend is totally sa

[gmx-users] problem linking fftw2 with gromacs 4.5.3

Hi folks, I'm experiencing some problem when I try to compile gromacs 4.5.3 linking fftw. This is the configure: > ./configure --prefix=/bgp/userinternal/cin0644a/gromacs.453 \ > --host=ppc --build=ppc64 --enable-ppc-sqrt=1 \ > --disable-ppc-altivec \ > --e

[gmx-users] [Fwd: Use an altenative folder for itp files]

Dear all, I have a little question about the use of a alternative localization of the ff librairy in GMX4.0.7. These (old) version of GMX is installed in a big cluster and i would like to use it for testing some CHARMM27 parameters. Since the charmm27.ff is not given this distribution, i wo

Re: [gmx-users] [Fwd: Use an altenative folder for itp files]

Stephane Abel wrote: Dear all, I have a little question about the use of a alternative localization of the ff librairy in GMX4.0.7. These (old) version of GMX is installed in a big cluster and i would like to use it for testing some CHARMM27 parameters. Since the charmm27.ff is not given

[gmx-users] Re: Can I have the mdp file?

Hi, I forward this discussion to the mailing list now because I think that it might be of interest to some people at least. Please find the mdp file of the GROMACS runs attached. To get the energies between GROMACS and CHARMM to match one has to do at least two things: * make sure the molecular

[gmx-users] domain decomposition error

Hi, I'm trying to run a simulation with 4.5.3 (double precision) on bluegene. I get this error: > NOTE: Turning on dynamic load balancing > > vol 0.35! imb F 54% pme/F 2.06 step 100, remaining runtime: 3 s > vol 0.33! imb F 48% pme/F 2.09 step 200, remaining runtime: 2 s > vol 0.35! imb

Re: [gmx-users] [Fwd: Use an altenative folder for itp files]

On 17/11/2010 10:59 PM, Stephane Abel wrote: Dear all, I have a little question about the use of a alternative localization of the ff librairy in GMX4.0.7. These (old) version of GMX is installed in a big cluster and i would like to use it for testing some CHARMM27 parameters. Since the cha

[gmx-users] Use an altenative folder for itp files

OK thank you for your help justin With the change you have suggested, grompp starts but an other error come quickly with the first line of the gb.itp: ERROR 1 [file /home/cont003/abel01/charmm27.ff//gb.itp, line 1]: Invalid directive implicit_genborn_params --

Re: [gmx-users] Use an altenative folder for itp files

Stephane Abel wrote: OK thank you for your help justin With the change you have suggested, grompp starts but an other error come quickly with the first line of the gb.itp: ERROR 1 [file /home/cont003/abel01/charmm27.ff//gb.itp, line 1]: Invalid directive implicit_genborn_params --

[gmx-users] PGI link error: unknown switch --rpath & attempted static link of dynamic object fftw/lib/libfftw3.so

Hi Roland, CMake works fine for the installation. There may be minor typos in the online installation instructions using CMake here http://www.gromacs.org/Developer_Zone/Cmake To use single precision FFTW, the two FFTW3 flags should be: cmake -D FFTW3F_INCLUDE_DIR=... -D FFTW3F_LIBRARIES=...

Re: [gmx-users] PGI link error: unknown switch --rpath & attempted static link of dynamic object fftw/lib/libfftw3.so

Yudong Sun wrote: Hi Roland, CMake works fine for the installation. There may be minor typos in the online installation instructions using CMake here http://www.gromacs.org/Developer_Zone/Cmake To use single precision FFTW, the two FFTW3 flags should be: cmake -D FFTW3F_INCLUDE_DIR=... -D

[gmx-users] Re: nve run of carbon nanotube

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Re: [gmx-users] Re: nve run of carbon nanotube

Adwait Mevada wrote: I would not say that you tube rotates so vigorously to be suspicious... The tube is also very small. What about trying a bigger one, e.g. with about 1 000 atoms? It should be more inert, if you'd like it to be such. ok. I will do that and tell you what happens. hope

[gmx-users] Re: gmx-users Digest, Vol 79, Issue 124

OK thank you all, I give up :-( a bientot Stephane Abel wrote: OK thank you for your help justin With the change you have suggested, grompp starts but an other error come quickly with the first line of the gb.itp: ERROR 1 [file /home/cont003/abel01/charmm27.ff//gb.itp, line 1]: Inva

[gmx-users] RE: Temperature Fluctuations

Hi, I am doing Replica Exchange (RE) simulations with 8 replicas 10 degree apart. My system has implicit solvent and there is only one molecule in the system (around 270 atoms). I am using Nose-Hover thermostat and tabulated potentials. When I do simulations with exchange frequency of 1 ns, the sy

[gmx-users] (no subject)

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[gmx-users] Error on Box Length when adding ions (gromacs 4.5.3/Charmm27/Tip3p)

I am having problems with grompp with my system. I am using Gromacs 4.5.3 FF = Charmm27 beta WT = TIP3P (recommended and its claimed its not too different than Charmms TIP3P) during minimization with pbc, I get the error about box length being small if I add neutralizing ions (I do not get t

Re: [gmx-users] Error on Box Length when adding ions (gromacs 4.5.3/Charmm27/Tip3p)

X Rules wrote: I am having problems with grompp with my system. I am using Gromacs 4.5.3 FF = Charmm27 beta WT = TIP3P (recommended and its claimed its not too different than Charmms TIP3P) during minimization with pbc, I get the error about box length being small if I add neutralizing io

[gmx-users] Error on Box Length when adding ions (gromacs 4.5.3/Charmm27/Tip3p)

Thanks Justin. Here is the quoted error: processing topology... Generated 2211 of the 2211 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2211 of the 2211 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' Excluding 2

Re: [gmx-users] Error on Box Length when adding ions (gromacs 4.5.3/Charmm27/Tip3p)

X Rules wrote: Thanks Justin. Here is the quoted error: /processing topology... Generated 2211 of the 2211 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2211 of the 2211 1-4 paramete

RE: [gmx-users] Error on Box Length when adding ions (gromacs 4.5.3/Charmm27/Tip3p)

> The error would imply that the box you have set up is < 2.0 nm, given the > cutoffs here. How did you define the box (editconf command)? What is your > box > size (last line of the .gro file or in the header of a .pdb)? > > -Justin okey.. I got it under control. The problem was. 1. crea

Re: [gmx-users] Error on Box Length when adding ions (gromacs 4.5.3/Charmm27/Tip3p)

X Rules wrote: > The error would imply that the box you have set up is < 2.0 nm, given the > cutoffs here. How did you define the box (editconf command)? What is your box > size (last line of the .gro file or in the header of a .pdb)? > > -Justin okey.. I got it under control. The pro

[gmx-users] Re: nve run of carbon nanotube

Also, as far as I understand, before NVE simulation, one should equilibrate the system in the NVT ensemble (at the desired T) and only then switch off T-coupling (=NVE). Vitaly Chaban >>> I would not say that you tube rotates so vigorously to be >>> suspicious... The tube is also very small. Wh

RE: [gmx-users] Error on Box Length when adding ions (gromacs 4.5.3/Charmm27/Tip3p)

> > There was a bug in an early 4.0.x feature that box vectors were not properly > written to .pdb files (CRYST line), but this was obviously fixed months, if > not > a year or more, ago. Gromacs tools are expected to handle numerous file > types > effortlessly, so using .gro is certainly

Re: [gmx-users] Error on Box Length when adding ions (gromacs 4.5.3/Charmm27/Tip3p)

X Rules wrote: > > There was a bug in an early 4.0.x feature that box vectors were not properly > written to .pdb files (CRYST line), but this was obviously fixed months, if not > a year or more, ago. Gromacs tools are expected to handle numerous file types > effortlessly, so using .gr

Re: [gmx-users] RE: Temperature Fluctuations

On 18/11/2010 3:28 AM, Nimesh Jain wrote: Hi, I am doing Replica Exchange (RE) simulations with 8 replicas 10 degree apart. My system has implicit solvent and there is only one molecule in the system (around 270 atoms). I am using Nose-Hover thermostat and tabulated potentials. When I do simu

Re: [gmx-users] domain decomposition error

On 18/11/2010 12:07 AM, Fabio Affinito wrote: Hi, I'm trying to run a simulation with 4.5.3 (double precision) on bluegene. Double precision comes with a big performance penalty, particularly on BlueGene. Don't use it unless you know you need it. I get this error: NOTE: Turning on dynami

[gmx-users] Re: nve run of carbon nanotube

Quoting gmx-users-requ...@gromacs.org: 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

Re: [gmx-users] Re: nve run of carbon nanotube

Adwait Mevada wrote: Quoting gmx-users-requ...@gromacs.org: 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 bod

[gmx-users] clusters of conformations of a molecular structure using g_cluster

Hi, gmx-users I want to know whether the g_cluster is appropriate to analyze clusters of conformations of a structure from a trajectory, and how to use it correctly to attain the right results? I try to analyze the clusters of conformations of a structure using g_cluster. But the outpu

[gmx-users] number of coordinates in pdb file does not match number of coordinates in topology file

Hi all!     I have this protein GFP that I'm working and right now a co-worker of mine is fixing the parameterization of the chromophore which is the middle of the protein and so my research professor asked me to run a simulation with the chromophore cut out of the protein. So I took my pdb fil

Re: [gmx-users] number of coordinates in pdb file does not match number of coordinates in topology file

Taylor Kaplan wrote: Hi all! I have this protein GFP that I'm working and right now a co-worker of mine is fixing the parameterization of the chromophore which is the middle of the protein and so my research professor asked me to run a simulation with the chromophore cut out of the prot

[gmx-users] Re: nve run of carbon nanotube

Date: Wed, 17 Nov 2010 15:08:02 -0500 >>> From: Vitaly Chaban >>> Subject: [gmx-users] Re: nve run of carbon nanotube >>> To: gmx-users@gromacs.org >>> Message-ID: >>> >>> Content-Type: text/plain; charset=3DISO-8859-1 >>> >>> Also, as far as I understand,

[gmx-users] Reg: Unit Of Surface Tension

Hi all What is the unit of Surface tension that one obtains from Gromacs using the g_energy command?. I searched the mailing list and i found two posts but the answers seems to be contradictory. Because in one post it was said that mN/m and in the other bar nm. below are the link of the two post.