Re: [gmx-users] g_analylse and g_energy give different average value

Li Jianguo wrote: Hi all, When I'm calculating the free energy by TI method and getting the average value of dv/dlamda, the two commands of g_analylse and g_energy give different average values, -0.0033 from g_energy and -0.049 from g_analyse. Which one should I follow? Anyone encounter the

Re: [gmx-users] Re: Energy Drift in Gromacs 4.0

Ilya Chorny wrote: Forgot column labels on energies. Average RMSD Fluct. Drift Tot-Drift 2 fs time step Total Energy46497.236445.6 2630.7 -148.833-148833 4 fs time step Total Energy

[gmx-users] g_analylse and g_energy give different average value

Hi all,   When I'm calculating the free energy by TI method and getting the average value of dv/dlamda, the two commands of g_analylse and g_energy give different average values, -0.0033 from g_energy and -0.049 from g_analyse. Which one should I follow? Anyone encounter the same problem? Thank

[gmx-users] Re: Energy Drift in Gromacs 4.0

Forgot column labels on energies. Average RMSD Fluct. Drift Tot-Drift2 fs time step Total Energy 46497.236445.6 2630.7 -148.833-148833 4 fs time step Total Energy41580.837693.42856.08 -13

[gmx-users] Energy Drift in Gromacs 4.0

Hello All, I am trying to run some calibration calculations with 2/4 fs time steps. I am trying to reproduce the results in the Gromacs 4.0 paper on a protein/water (not the same protein) system with ~100K atoms. I ran 1 ns simulation in the NVE ensemble. My mdp params are shown below. Topolgy was

Re: [gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3

Claus Valka wrote: Dear gromacs users, I sent this e-mail as how someone can avoid an error that occured during a simulation. The solution I proposed was just increasing the tables extention parameter in the mdp file. The error concerned the bonded interactions and it had to do with bad equil

RE: [gmx-users] How to overcome Fatal error of bonded interactions Gromacs 4.0.3

Dear gromacs users, I sent this e-mail as how someone can avoid an error that occured during a simulation. The solution I proposed was just increasing the tables extention parameter in the mdp file. The error concerned the bonded interactions and it had to do with bad equilibration resulting in

[gmx-users] Infiniband Hardware

I am about to purchase some infiniband hardware and was wondering if anybody on the mailing list has experience/insight into what kinds of hardware to buy and what to stay away from. Thanks, Ilya -- Ilya Chorny Ph.D. ___ gmx-users mailing listgmx-

Re: [gmx-users] Calculate asphericity of a group of atoms

Hi Loan, you could calculate the radii of gyration about the principal axes using the "-p" option of the analysis program "g_gyrate". The ratio of the largest and smallest eigenvalues (essentially the radii of gyration along the principal axes) could serve as an "asphericity" index. Regards, Su

[gmx-users] Calculate asphericity of a group of atoms

Hi everyone, I would like to measure the asphericity of a group of atoms. Base on literature searching results, there are studies measure the asphericity using the radius of gyration tensor, compute the eigenvalues of this tensor, and use these eigenvalues to compute asphericity (0<=delt

Re: [gmx-users] Fatal error: 2 atoms are not part of any of the T-Coupling groups during md simulation.

Thanks a lot to both of you. Chitrita. On Wed, Mar 11, 2009 at 2:09 AM, Justin A. Lemkul wrote: > > > Chitrita Dutta Roy wrote: > >> Hi Tsjerk, >> >> Did you mean to send you the md.mdp file that I used to run grompp for md >> simulation? I am using Gromacs 4.0.2 versision. I am not very clear

Re: [gmx-users] Fatal error: 2 atoms are not part of any of the T-Coupling groups during md simulation.

Chitrita Dutta Roy wrote: Hi Tsjerk, Did you mean to send you the md.mdp file that I used to run grompp for md simulation? I am using Gromacs 4.0.2 versision. I am not very clear about the parameters used in mdp files. So I am sending the mdp file here. Some consultation with the manual

Re: [gmx-users] Fatal error: 2 atoms are not part of any of the T-Coupling groups during md simulation.

Hi Chitrita, > I am not very clear about the parameters used in mdp files. So I am sending > the mdp file here. This is of course vital when performing simulations. Do read up on these things. This is the part of the .mdp file that determines the how and what of temperature coupling: > ; Beren

Re: [gmx-users] Fatal error: 2 atoms are not part of any of the T-Coupling groups during md simulation.

Hi Tsjerk, Did you mean to send you the md.mdp file that I used to run grompp for md simulation? I am using Gromacs 4.0.2 versision. I am not very clear about the parameters used in mdp files. So I am sending the mdp file here. cpp = /usr/bin/cpp constraints = all-bonds

Re: [gmx-users] Cuda support

Jack Shultz wrote: Has anyone used these binaries? How are they? Any recommendations on using GPUs? https://simtk.org/project/xml/downloads.xml?group_id=161#package_id600 Those binaries are just about useless. From their README... - Gromacs-OpenMM Preview Release 2 Gromacs-OpenMM

[gmx-users] Problems with pulling code

Hi there, I used the old Gromacs 3.3 for pulling simulations using afm with success. For the new upgrade, I cannot understand the new configuration for the former standard afm constant velocity pulling with one reference group and the pulling group. For example, when the manual says position

[gmx-users] Cuda support

Has anyone used these binaries? How are they? Any recommendations on using GPUs? https://simtk.org/project/xml/downloads.xml?group_id=161#package_id600 -- Jack http://www.facebook.com/home.php#/profile.php?id=832713248 http://hydrogenathome.org ___ gm

Re: [gmx-users] Simulated annealing

jayant james wrote: Hi! So the part of my pr.mdp files that handles pressure and temperature looks like as below and if I were to create an index file by name "N-extension" an type it next in the tc-grps as N-extension along with the existing Protein Non-Protein groups is this how I get to h

Re: [gmx-users] Simulated annealing

Hi! So the part of my pr.mdp files that handles pressure and temperature looks like as below and if I were to create an index file by name "N-extension" an type it next in the tc-grps as N-extension along with the existing Protein Non-Protein groups is this how I get to handle the simulated anneali

Re: [gmx-users] Fatal error: 2 atoms are not part of any of the T-Coupling groups during md simulation.

Hi Chitrita, You'll have to make sure that whatever t-coupling groups you've specified (referring to groups in pr.ndx) together capture all atoms. This stands apart from the topology and coordinates. If you're not sure, paste the temperature related mdp options for us to be able to help you furthe

Re: [gmx-users] Fatal error: 2 atoms are not part of any of the T-Coupling groups during md simulation.

Chitrita Dutta Roy wrote: --- Program grompp, VERSION 4.0.2 Source code file: readir.c, line: 1050 Fatal error: 2 atoms are not part of any of the T-Coupling groups --- Even the .top file

[gmx-users] Fatal error: 2 atoms are not part of any of the T-Coupling groups during md simulation.

I am performing grompp for md simulation after position restrained MD. Before final md simulation by grompp I have made pr.ndx file and did necessary corrections in it to insert added Na+ to be counted properly. But after running the following command - grompp -f md.mdp -c pr.gro -p scr8.top -o md

Re: [gmx-users] Potential energy of a single amino acid residu

Tom Venken wrote: Mu-Z Coul-SR:r_8-r_8 LJ-SR:r_8-r_8 LJ-LR:r_8-r_8 Coul-14:r_8-r_8 LJ-14:r_8-r_8 Coul-SR:r_8-rest LJ-SR:r_8-rest LJ-LR:r_8-restCoul-14:r_8-rest LJ-14:r_8-restCoul-SR:rest-rest LJ-SR:rest-rest LJ-LR:rest-rest Coul-14:rest-rest LJ-14:rest-re

[gmx-users] g_sdf gives wrong refmol with multiple center molecules

Hi, if you give g_sdf just one molecule (in mode 1) to look at the distribution of other atoms around it, everything looks fine. However, if you give two or more molecules, the refmol.gro that is printed is messed up, but the actual density map still looks ok. You can try this with the 216 wa

Re: [gmx-users] Potential energy of a single amino acid residu

I get the following list: Angle Proper-Dih. Ryckaert-Bell.LJ-14 Coulomb-14LJ-(SR) LJ-(LR) Coulomb-(SR) Coul.-recip. Potential Kinetic-En. Total-Energy Temperature Pressure-(bar)Box-X Box-Y Box-Z

Re: [gmx-users] question about parallel runing of gromacs

Xiang Mao wrote: I got something like this in log file Host:XXX pid:5504 nodeid :0 nnodes:1 and I think I compiled mdrun_mpi using --enable-mpi. I am wondeirng if I should use lam_mpi instead of MPICH2? It is better to *know* than to *think.* Did you try what was suggested to you

Re: [gmx-users] question about parallel runing of gromacs

I got something like this in log file Host:XXX pid:5504 nodeid :0 nnodes:1 and I think I compiled mdrun_mpi using --enable-mpi. I am wondeirng if I should use lam_mpi instead of MPICH2? thanks. On Mon, Mar 9, 2009 at 11:03 PM, Diego Enry Gomes wrote: > On Mar 9, 2009, at 5:12 PM, Mark Abra

[gmx-users] Re: Fwd: gmx-users Digest, Vol 59, Issue 74

Thanks for your reminder! javacfish --- li i think if you use -maxwarn 1, that's fine only for this time only. Actually you will also get the same prob later at the when using posre.mdp and also mdrun.mdp ..if you still you the old mdp file. the be

Re: [gmx-users] relative constraint deviation after lincs

Alessandro Casoni wrote: hi users, I want to simulate a position restraint md. pdb2gmx creates a correct protein.top and a posre.itp file. but when I use " define = -DPOSRES" I have this error: Step 1004, time 2.008 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.026978,

[gmx-users] relative constraint deviation after lincs

hi users, I want to simulate a position restraint md. pdb2gmx creates a correct protein.top and a posre.itp file. but when I use " define = -DPOSRES" I have this error: Step 1004, time 2.008 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.026978, max 1.366297 (between atoms

Re: [gmx-users] Re: problems with editconf command

Justin A. Lemkul wrote: The initial conf.gro and topol.top are also attached. These are not useful for diagnosis; the screenshot is enough. I'll take that back. I looked a bit closer at the screenshot, and it appeared that there were several atoms floating off into nowhere. Sure enough

Re: [gmx-users] Problem to simulate silica melts and amorphous silica with BKS potentials

David Waroquiers wrote: Hello I'm trying to simulate amorphous SiO2 with the use of the BKS potentials (van Beest, B. W. H.; Kramer, G. J. & van Santen, R. A. - Phys. Rev. Lett., American Physical Society, 1990, 64, 1955-1958). According to these potentials, I should use the Buckingham potentia

Re: [gmx-users] Cannot obtain the expected pressure using the Parrinello-Rahman coupling in a gas-liquid system

GuoGuangjun wrote: compressibility = 0.0 4.5e-3 You have set zero compressibility in the x-y direction, so you get... Box-X 2.94006 0 0 0 0 Box-Y 2.94006 0 0 0 0

[gmx-users] Re: problems with editconf command

Please keep correspondence on the list. If you want to post images, do so via the web so that everyone can have a look. Andrew Voronkov wrote: Dear Justin, I am very sorry for writing to you directly, but seems like gmx user list doesn't like attachments. I have problems with editconf comma

Re: [gmx-users] Potential energy of a single amino acid residu

Tom Venken wrote: Hello, I am trying to calculate the potential energy of an individual amino acid and its interaction energy with the rest of the protein. I have found another user with a similar problem: http://www.gromacs.org/pipermail/gmx-users/2007-May/027114.html so I tried to follow th

Re: [gmx-users] pdb2gmx -vsite h hangs

Ilya Chorny wrote: Justin, Thanks for pointing me to section 6.5. I am running ~500K atoms because I want to test the scaling as well. What I mean was, when reporting problems to the list, make the test case small so you eliminate variables like available system memory. Furthermore, it

[gmx-users] Problem to simulate silica melts and amorphous silica with BKS potentials

Hello I'm trying to simulate amorphous SiO2 with the use of the BKS potentials (van Beest, B. W. H.; Kramer, G. J. & van Santen, R. A. - Phys. Rev. Lett., American Physical Society, 1990, 64, 1955-1958). According to these potentials, I should use the Buckingham potentials with user-defined param

RE: SV: SV: SV: [gmx-users] g_order version 4.0.x

I have now made a new .ndx file as written in the wiki - and it works!!! :-) Thank you very much for your time Justin, I think what had confused my was the way the .ndx file was made in 3.3.3 and then the previous threads about the "new way" to make .ndx file in gromacs 4.0.x Anyway, I'm very hap

[gmx-users] Potential energy of a single amino acid residu

Hello, I am trying to calculate the potential energy of an individual amino acid and its interaction energy with the rest of the protein. I have found another user with a similar problem: http://www.gromacs.org/pipermail/gmx-users/2007-May/027114.html so I tried to follow the same procedure

RE: [gmx-users] Cannot obtain the expected pressure using the Parrinello-Rahman coupling in a gas-liquid system

On Tue, 2009-03-10 at 09:46 +, GuoGuangjun wrote: > Hi, > > According to Berk's instructions, I first run a 5 ns-long berendesen > P-coupling simulation, and then change to Parrinello-Rahman coupling > for another 5 ns. The parameters and results are listed in the > following. My question is

RE: [gmx-users] Cannot obtain the expected pressure using the Parrinello-Rahman coupling in a gas-liquid system

Hi, According to Berk's instructions, I first run a 5 ns-long berendesen P-coupling simulation, and then change to Parrinello-Rahman coupling for another 5 ns. The parameters and results are listed in the following. My question is why the average pressures in the X- and Y-directions is not

[gmx-users] "Gromacs 4 grompp -v" err

Hello,everyone! Sorry for the last letter! I have install gromacs4, but when I stury the tutor of gromacs, and input command "grompp -v in every examples", the err be engenderred as below: l...@localhost water]$  grompp -v :-)  G  R  O  M  A  C  S  (-:    Go

Re: [gmx-users] Gromac4 grompp -v Err

li bai wrote: Hello,everyone! I have install gromacs4, but when I stury the tutor of gromacs, and input command "grompp -v in every examples", the err be engenderred as below: There were 2 notes There was 1 warning --- Program grompp, VER

Re: [gmx-users] Gromac4 grompp -v Err

Hi Li Bei, You're using an old .mdp parameter file. Use a new one. If you make an empty .mdp file (touch empty.mdp) and use it as input to grompp, a .mdp file with all parameters set to default will be generated (mdout.mdp). Cheers, Tsjerk On Tue, Mar 10, 2009 at 9:59 AM, li bai wrote: > Hello

[gmx-users] Gromac4 grompp -v Err

Hello,everyone! I have install gromacs4, but when I stury the tutor of gromacs, and input command "grompp -v in every examples", the err be engenderred as below: l...@localhost water]$  grompp -v :-)  G  R  O  M  A  C  S  (-:    Go Rough, Oppose Many Angry Ch

Re: [gmx-users] do_dssp fatal error

Did you download the "dssp" software from here ? http://swift.cmbi.ru.nl/gv/dssp/HTML/dsspcmbi On Mar 10, 2009, at 1:12 AM, Homa Azizian wrote: Hi when I use do_dssp the following error come: Program do_dssp, VERSION 4.0.3 Source code file: do_dssp.c, line: 471 Fatal error: Failed to execu

Re: [gmx-users] problem in pdb file after SA

You mean that half the protein is in one side of your cubic box and the other half is on the other side ? Try removing PBC or fitting to a reference frame (like the one before SA). Search the list archives, this is a very common question. On Mar 9, 2009, at 10:17 PM, Homa Azizian wrote: I

[gmx-users] do_dssp fatal error

Hi when I use do_dssp the following error come: Program do_dssp, VERSION 4.0.3 Source code file: do_dssp.c, line: 471 Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddS7CWeR dd48KVro > /dev/null 2> /dev/null How could I fix this. Thank you in advance. -- Tehran University o

Re: [gmx-users] Isn't dt=0.0001 very small?

Hi Andrew, I have just repeated this tutorial. There is nothing wrong with that. Download all the files again and repeat the tutorial from the beginning. It can be a file that was corrupted during your previous download or you did something wrong in one of the steps. You can copy&paste the

[gmx-users] problems with pulling direction and the initial spring position

Hello GMX user, I want to pull a compound named UNK (whose initial center of mass is X1, Y1, Z1) through a nanotube named STACK(whose center of mass is X2, Y2, Z2). The final position of UNK is supposed to be around X3, Y3, Z3. I used the pull.ppa file as follows: ngroups = 1 g

Re: [gmx-users] Isn't dt=0.0001 very small?

Hi Andrew, > I'm doing this tutorial: > https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf > and I have an error with dt=0.002 or even dt=0.001 in pr.mdp during > equilibration. It works only with dt=0.0001 which seems very very small step > for me. Your observation is correct:

[gmx-users] Isn't dt=0.0001 very small?

Dear GROMACS users, I'm doing this tutorial: https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf and I have an error with dt=0.002 or even dt=0.001 in pr.mdp during equilibration. It works only with dt=0.0001 which seems very very small step for me. Is it ok or I need to clean up