Re: [gmx-users] error in ATOM2CG.awk script

sunny mishra wrote: Yeah I agree wiht you but I tested another protein as well 1BL8 to check if there was a problem specifically in 1K4C. Even after testing 1BL8 it gives me the same error. What do you think? 1BL8 has a huge amount of atoms missing in the crystal structure, too. Be aware

Re: [gmx-users] optimization of gromacs 4.0.5 on AIX Power6

Rodrigo faccioli wrote: I believe that this problem is about mpi installation. What mpi version was installed ? Lampi or openmpi. That would be plausible on a home-built linux cluster, but not so likely on a cluster bought from a recognized vendor like IBM, whose MPI installation should be d

Re: [gmx-users] error in ATOM2CG.awk script

sunny mishra wrote: Dear all, I was earlier facing problem regarding the mismatch of atoms in .top and .gro file and then after useful discussion here I figured out that some atoms were missing in my cg.pdb file and that problem is because of the OLDER atom2cg.awk script which MARTINI folks

Re: [gmx-users] LINCS

tekle...@ualberta.ca wrote: Hi Justin, "There is something physically unrealistic about your model" You are right! The main problem I found out is that some of the structures in my Solution broke down.. I used ... genbox -cp .grob -nmol 20 -ci insert.gro -cs spc216.gro XXX.top -

[gmx-users] error in ATOM2CG.awk script

Dear all, I was earlier facing problem regarding the mismatch of atoms in .top and .gro file and then after useful discussion here I figured out that some atoms were missing in my cg.pdb file and that problem is because of the OLDER atom2cg.awk script which MARTINI folks have in their website. When

[gmx-users] Re: wierd behavior of mdrun

Then I believe you have problems with MPI. Before I experienced something alike on our old system - serial version worked OK but parallel one failed. The same issue was with CPMD by the way. Another programs worked fine. I didn't correct that problem... On Thu, Aug 27, 2009 at 7:14 PM, Paymon Pir

Re: [gmx-users] Using make_ndx

Lili Peng wrote: Hi everyone, I'm trying to figure out the right commands for make_ndx so to generate the correct index.ndx file for g_bond analysis. From my PDB file: ATOM 1 BN0 GGA X 1 107.255 17.133 66.368 1.00 0.00 P1 C ATOM 2 SC1 GGA X 1 110.304 14

[gmx-users] Using make_ndx

Hi everyone, I'm trying to figure out the right commands for make_ndx so to generate the correct index.ndx file for g_bond analysis. From my PDB file: ATOM 1 BN0 GGA X 1 107.255 17.133 66.368 1.00 0.00 P1 C ATOM 2 SC1 GGA X 1 110.304 14.942 66.116 1.00 0.00

[gmx-users] Re: g_energy and g_analyze give different averages

Is there a correct way to obtain the standard deviation for these data sets? > > Ragnarok sdf wrote: > > When analysing FEP simulations. After running g_energy -f fep000.edr -f2 > > fep_000-005.edr for obtaining the dF = -kT ln < exp(-(EB-EA)/kT) >A I > tried > > to obtain the standard deviation

Re: [gmx-users] wierd behavior of mdrun

One more point: when I run the job interactively, although it works but date and time are wrong! step 0 step 100, will finish Wed Sep 16 16:16:00 2009 step 200, will finish Wed Sep 16 14:32:34 2009 step 300, will finish Wed Sep 16 13:57:51 2009 step 400, will finish Wed Sep 16 11:35:46 2009 step 5

Re: [gmx-users] g_energy and g_analyze give different averages

Ragnarok sdf wrote: When analysing FEP simulations. After running g_energy -f fep000.edr -f2 fep_000-005.edr for obtaining the dF = -kT ln < exp(-(EB-EA)/kT) >A I tried to obtain the standard deviation for this ensemble average using g_analyze -f runavg.xvg, but I've noticed that the average valu

[gmx-users] g_energy and g_analyze give different averages

When analysing FEP simulations. After running g_energy -f fep000.edr -f2 fep_000-005.edr for obtaining the dF = -kT ln < exp(-(EB-EA)/kT) >A I tried to obtain the standard deviation for this ensemble average using g_analyze -f runavg.xvg, but I've noticed that the average values are quite different

RE: [gmx-users] Pressure for froozen atoms

That's enough for the non-bonded interactions. Energy group exclusions work on both the energy and the forces. But if you have bonded interactions between atoms in S you also need to exclude those. Note that this only matters if you want to have the pressure. Berk > From: yel...@uni-mainz.de >

Re: Re: [gmx-users] is the D G sol of g_sas useless? why?

Is true, the paper is old, but is an simply aproximation Besides that, do you know other simply way for protein-protein DG bind from dynamics (but not g_lie) ? Thanks anyway - Felipe Villanelo Lizana Biochemist Laboratorio de Biología Estructural y Molecular Universidad de Chile

RE: [gmx-users] table extension

There is a misunderstanding here about noticing. For efficiency reasons, the code does not check if atoms are beyond the table length. So the code does not care about or notice anything. However, you do care, since you do not want random forces. (Although in nearly all cases the force will be, o

Re: [gmx-users] table extension

But what if the gmx code did notice it? Koby Levy research group, Weizmann Institute of Science. FAX: 972-77-444-7905 http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Thu, Aug 27, 2009 at 16:21, Mark Abraham wrote: > It would look up a non-random energy and force. If the code never noticed

RE: [gmx-users] Pressure for froozen atoms

Hi together, > You have to make sure that you do not calculate forces between frozen atoms, is it enough to include in grompp.mdp such command: ; Non-equilibrium MD stuff freezegrps = S freezedim= Y Y Y ;Energy group exclusion for position restraints energygrps

RE: Re : [gmx-users] PULL CODE AND NpT ensemble

Hi, There are no settings that matter in particular for pulling compared to a normal simulation. All the settings that matter normally matter here as well. NVT pulling should give nearly identical results no NPT, as long as you set the volume correctly. Berk To: gmx-users@gromacs.org Subject:

Re: [gmx-users] table extension

Omer Markovitch wrote: Thanks. And what happens if later on it comes back to the cut-off + table-extension range? It would look up a non-random energy and force. If the code never noticed the distance was out-of-range, it won't notice it come back into range either. Mark Koby Levy researc

RE: [gmx-users] Pressure for froozen atoms

Hi, Gromacs does not do anything special for frozen atoms. You have to make sure that you do not calculate forces between frozen atoms, if you want the virial to be correct. Berk > Date: Thu, 27 Aug 2009 14:46:47 +0200 > From: alexander.h...@mytum.de > To: gmx-users@gromacs.org > Subject: [gmx-

[gmx-users] Pressure for froozen atoms

Hi guys, does gromacs use the following scheme to calculate the virial/pressure for systems including froozen atoms: http://www.ccp5.ac.uk/infoweb/wsmith22/wsmith22/wsmith22.html ?? Thx, Alex ___ gmx-users mailing listgmx-users@gromacs.org http://li

Re: [gmx-users] optimization of gromacs 4.0.5 on AIX Power6

I believe that this problem is about mpi installation. What mpi version was installed ? Lampi or openmpi. There is a good tutorial about that in http://www.gromacs.org/WIKI-import/Quick_and_Dirty_Installation Best regards, -- Rodrigo Antonio Faccioli Ph.D Student in Electrical Engineering Unive

Re: [gmx-users] table extension

Thanks. And what happens if later on it comes back to the cut-off + table-extension range? Koby Levy research group, Weizmann Institute of Science. FAX: 972-77-444-7905 http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Thu, Aug 27, 2009 at 11:13, Berk Hess wrote: > A interaction beyond the c

Re: [gmx-users] optimization of gromacs 4.0.5 on AIX Power6

Silvia Giuliani wrote: Dear All Has anybody tried version 4.0.5 on an IBM Power6 (4.7Ghz) cluster? We have installed the program with the following configure options (using fftw we installed separately): ./configure --with-fft=fftw2 --enable-mpi --enable-float CC=mpcc_r F77=mpxlf_r CXX=mpCC_

Re : [gmx-users] PULL CODE AND NpT ensemble

Hi Berk, Thanks for your answer. I just want to be sure that the procedure is correct. No I do not look at the pressure/volume fluctutation. But I do want to make a clever choice of the ensemble so that no significant extra artifact are generated, since the number of contraint to be calculated

RE: [gmx-users] PULL CODE AND NpT ensemble

Hi, I would use v-rescale and Berendsen pressure coupling. Although Berendsen pressure coupling, strictly speaking, does not give the correct ensemble, in practice it produces negligible artifacts, unless you are looking at pressure/volume fluctuations. Berk To: gmx-users@gromacs.org Date: Th

Re: [gmx-users] grompp.mdp

Hi kayal, Well, given that it reads "Fatal error" your final question seems a bit odd, doesn't it? How did you obtain the topology? Apparently, there's a bit more specified in it than a single butane! Besides, I notice that you use the GROMOS force field, which is a united atom force field. That m

[gmx-users] PULL CODE AND NpT ensemble

Hi all, I would like to use pull code to evaluate the free energy of pulling system1 from system2. Free energy calculation should be done for NpT ensemble. All tutorials found for calculating free energy used 1) berensen for T and P coupling or 2) berensen for T coupling AND Parrinelo for P cou

[gmx-users] grompp.mdp

Hi, I am going to analyse the normal mode analysis of n-butane. For this I donloaded a PDB id .Then opened in wordpad and just took the glu residue.Opend it on viewerpro and deleted the -COO, NH2,-CH2 portion to make it n-butane.Then made a pdb file and ran in GROMACS. I suceesfully created the to

[gmx-users] optimization of gromacs 4.0.5 on AIX Power6

Dear All Has anybody tried version 4.0.5 on an IBM Power6 (4.7Ghz) cluster? We have installed the program with the following configure options (using fftw we installed separately): ./configure --with-fft=fftw2 --enable-mpi --enable-float CC=mpcc_r F77=mpxlf_r CXX=mpCC_r CFLAGS="-O3 -qarch=pwr

RE: [gmx-users] table extension

Hi, No, this is not correct. A interaction beyond the cut-off + table-extension will get a random energy and force depending on what is stored in the memory of your computer beyond the table___ gmx-users mailing listgmx-users@gromacs.org http://lis

Re: [gmx-users] table extension

Thanks Mark. I am simulating a dimer in vacuum, and it is my understanding that once a non-bonded interaction has exceeded the table-extension cutoff this interaction will NOT be included in the potential for the remaining simulation, even if it will later come back to a distance within the table-e