Re: [gmx-users] Lincs all-bonds causing instability in otherwise stable system

Thanks Mark, A grompp warning about problematic constraints sounds like a good idea. DMSO is actually tetrahedral, not planar. Is that possible (and hopefully straightforward) to do with virtual sites? If it is, is there an example I could look at? Thanks, Cara From:

[gmx-users] How to proceed with molecule.itp file

Hi, I have made a molecule.itp file according to the chapter 5 of Gromacs Manual and existing entries in the ff directory I want to use. My problem is that I don't know how to continue, in theory I have to include it in the .top file but a .top file is produced by pdb2gmx which I cannot use

[gmx-users] pdb2gmx: Can I change the margin 10% to a higher value in the specbond.dat ?

Dear GROMACS experts, I am using pdb2gmx for a protein with 5 disulfind bond https://copy.com/kPLlSianI4LtohNy The distance between each Cys SG are: 0.203, 0.204, 0.204, 0.205, 0.167. As a result, 10% margin of any value of the reference length in specbond.dat cannot cover all of the 5 Cys

[gmx-users] tpr file portability

Dear All, I am generating .tpr file on my desktop (UBUNTU 14.04 X86_64) and running MD on Cray (suse-linux X86_64 )using Gromacs-5.0.5. It is mentioned on the Gromacs site is that Generally the tpr file is very portable between different machines. Is it valid in my case? Is there anything to

Re: [gmx-users] tpr file portability

Hi, There are no known issues with .tpr file portability. By design there should be none. Mark On Thu, May 21, 2015 at 11:41 AM Satyabrata Das satyabrata...@gmail.com wrote: Dear All, I am generating .tpr file on my desktop (UBUNTU 14.04 X86_64) and running MD on Cray (suse-linux X86_64

[gmx-users] .gro error

Hello, i'm working on membrane thickness in Martínez-Seara dppc article. When i use the following command: printf %s\n r 1-64 a P r 65-128 a P q|make_ndx -f dppc128_1.gro -o Dpp.ndx The following error appears: File Input/output error: dppc128_1.gro. Could you help me to solve it please?

Re: [gmx-users] .gro error

On 5/21/15 2:30 PM, Poncho Arvayo Zatarain wrote: Hello, i'm working on membrane thickness in Martínez-Seara dppc article. When i use the following command: printf %s\n r 1-64 a P r 65-128 a P q|make_ndx -f dppc128_1.gro -o Dpp.ndx The following error appears: File Input/output error:

Re: [gmx-users] links errors at 700 or 800 K

On 5/21/15 10:24 AM, Christopher Neale wrote: Dear Users: I have a system with an 8-mer peptide in a box of water. After a 2-ns npt equilibration, I run 100 ns of nvt at various temperatures (300-800 K) in preparation for a REMD simulation. I am using velocity langevin for temperature

[gmx-users] Version 100 with version 83 program

I' m running Martínez Seara dppc tutorial and when i use echo 0|trjconv -f dppc128_1.xtc -s dppc128_1.tpr -o dppc128_1-ini.gro -dump 10 it appears the following error: Fatal error: reading tpx file (dppc128_1.tpr) version 100 with version 83 program. I' m using Gromacs 4.6.5 maybe it has to be

Re: [gmx-users] Segmentation fault (core dumped) version 4.6.*

Dear Chris, Thanks a lot for your reply. Indeed, my first files were create by using gromacs 5, so i created all of the files again, but now using 4.6.3 version. Sadly the error is still appearing :/ (Even using gmxcheck) :-) gmxcheck (-: Option Filename

Re: [gmx-users] About Tabulated Potentials

On 5/21/15 8:36 AM, zhangzhengc wrote: Dear all, I want to add the Morse potential for nonbonded interactions between CH4 and CH4. I used three table files each contain seven columns to add the H to H, H to C, and C to C Morse form interactions. I set Coulombtype=user, vdwtype=user , and

[gmx-users] Reading double-precision trr file using xdrfile

Dear Gromacs developers and users, I would like to read a .trr trajectory file in double-precision after running a simulation in double-precision, however reading the atomic positions etc with the xdrfile appears to yield only single precision. Are the trajectory position, velocity and forces

[gmx-users] Version 100 with version 83 program

I' m running Martínez Seara dppc tutorial and when i use echo 0|trjconv -f dppc128_1.xtc -s dppc128_1.tpr -o dppc128_1-ini.gro -dump 10 it appears the following error: Fatal error: reading tpx file (dppc128_1.tpr) version 100 with version 83 program. I' m using Gromacs 4.6.5 maybe it has to be

Re: [gmx-users] How to proceed with molecule.itp file

On 5/21/15 8:00 AM, Sotirios Dionysios I. Papadatos wrote: Hi, This indeed begins to clarify things but just to make sure I got it right. I want to simulate only a specific molecule from a protein, meaning I took the initial protein and deleted everything but the molecule. So I use the

Re: [gmx-users] How to proceed with molecule.itp file

Hi, This indeed begins to clarify things but just to make sure I got it right. I want to simulate only a specific molecule from a protein, meaning I took the initial protein and deleted everything but the molecule. So I use the pdb2gmx to the molecule, I edit the topol.top that is produced

[gmx-users] About Tabulated Potentials

Dear all, I want to add the Morse potential for nonbonded interactions between CH4 and CH4. I used three table files each contain seven columns to add the H to H, H to C, and C to C Morse form interactions. I set Coulombtype=user, vdwtype=user , and Dispcorr = no, and add energrps and

Re: [gmx-users] Ligand covalently bound to protein: Best practice

Thanks for your comment and sorry for my weird english. I must have been in my thoughts :). I was also wondering if I attach covalently a protein to another protein or a large organic molecule through a residue in the middle of the sequence my approach would not work. Does anyone have a

Re: [gmx-users] Ligand covalently bound to protein: Best practice

On 5/21/15 4:51 PM, Ebert Maximilian wrote: Thanks for your comment and sorry for my weird english. I must have been in my thoughts :). I was also wondering if I attach covalently a protein to another protein or a large organic molecule through a residue in the middle of the sequence my

[gmx-users] PMF calculation with constraint distance

Hi all, I started to calculate PMF between two ions in solution and I used constraint for pull option, instead of umbrella as I saw in Umbrella sampling Tutorial of Justin. This is the part of my mdp file! ; Pull code pull= constraint; Justin's value was umbrella pull_geometry

Re: [gmx-users] PMF calculation with constraint distance

On 5/21/15 5:00 PM, leila salimi wrote: Hi all, I started to calculate PMF between two ions in solution and I used constraint for pull option, instead of umbrella as I saw in Umbrella sampling Tutorial of Justin. This is the part of my mdp file! ; Pull code pull= constraint;

Re: [gmx-users] About Tabulated Potentials

On 5/21/15 3:46 PM, Zhengcai Zhang wrote: Dear Justin, Thank you for your reply. When I choose l-J form potential for the non-bonded interactions between CH4 and CH4 using the parameters from another paper, I can get system pressure (25.5Mpa) in accord with experimental value at same

Re: [gmx-users] Version 100 with version 83 program

On 5/21/15 3:02 PM, Poncho Arvayo Zatarain wrote: I' m running Martínez Seara dppc tutorial and when i use echo 0|trjconv -f dppc128_1.xtc -s dppc128_1.tpr -o dppc128_1-ini.gro -dump 10 it appears the following error: Fatal error: reading tpx file (dppc128_1.tpr) version 100 with version 83

Re: [gmx-users] PMF calculation with constraint distance

Thanks Justin. Yes I have done PMF with Blue moon ensemble with DFT. Now I want to do the same with gromacs to have some knowledge about my FF parameters and compare with my DFT results! You meant I have to do with different configuration and average the forces? I am wondering that I did in DFT

[gmx-users] Ligand covalently bound to protein: Best practice

Hi there, I am about to setup a protein ligand complex in which the the amino acid is covalently bound to the ligand. What I was about to do is to build an artificial amino acid (in this case serine) with the ligand attached to it an derive partial charges using antechamber or the RED server.

Re: [gmx-users] Ligand covalently bound to protein: Best practice

On 5/21/15 4:30 PM, Ebert Maximilian wrote: Hi there, I am about to setup a protein ligand complex in which the the amino acid is covalently bound to the ligand. What I was about to do is to build an artificial amino acid (in this case serine) with the ligand attached to it an derive

Re: [gmx-users] tpr file portability

Thank you sir. Best regards, Satyabrata Das -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit

Re: [gmx-users] How to proceed with molecule.itp file

Hi Sotirios, You need to either edit the .top file produced by pdb2gmx or make your own from scratch. You only need the pdb2gmx output if your system includes standard amino acids. If you have both a standard protein and a non-standard molecule, you should make a .pdb file with just the

Re: [gmx-users] pdb2gmx: Can I change the margin 10% to a higher value in the specbond.dat ?

Hi Cheng, You can add another entry for a disulfide bond with a different length. Cheers, Tsjerk On Thu, May 21, 2015 at 11:31 AM, Zhang, Cheng c.zhang...@ucl.ac.uk wrote: Dear GROMACS experts, I am using pdb2gmx for a protein with 5 disulfind bond https://copy.com/kPLlSianI4LtohNy

Re: [gmx-users] build nuance in gmx5 (avoiding file INSTALL cannot find gmx)

You can't install into the build tree, AFAIK that's not allowed! Install into a clean target directory instead. Also, you mkdir source; mv * source step is just weird. Why move the source around? Instead you can simply create a build directory - this can even be in the source tree just as the

[gmx-users] pdb2gmx: can we use a file to specify the protonation instead of using -inter?

Dear GROMACS experts, Can I ask is there a more efficient way to deal with the -inter option in the pdb2gmx command? Now, I have to manually assign individual protonation status one by one, which takes a very long time. Sometimes I make a mistake and I have to re-do all of them again.

[gmx-users] links errors at 700 or 800 K

Dear Users: I have a system with an 8-mer peptide in a box of water. After a 2-ns npt equilibration, I run 100 ns of nvt at various temperatures (300-800 K) in preparation for a REMD simulation. I am using velocity langevin for temperature control. Everything is fine for =600 K. Above that,

Re: [gmx-users] pdb2gmx: can we use a file to specify the protonation instead of using -inter?

Dear Cheng: You can define protonation states like this: echo 0 1 2 | pdb2gmx -ff amber99sb-ildn -water tip3p -his That will give you, in order for three HIS residues: 0. H on ND1 only (HID) 1. H on NE2 only (HIE) 2. H on ND1 and NE2 (HIP) You can also use -inter, but you'll need to do a

[gmx-users] build nuance in gmx5 (avoiding file INSTALL cannot find gmx)

Dear Users: This is just a note about compiling gromacs 5 so that the solution can be found by others if they need it. I used to compile gromacs like this: download and unpack tarball cd gromacs-5.0.5 mkdir source mv * source mkdir exec cd exec ** run my build script from here, using

Re: [gmx-users] Generate the water box

Dear all, I can generate the cubic box or the rectangular box with gmx solvate -cs water.gro -box but I would like to have the octahedron box.I try many way but I can not. How I can do it? Thank a lot Tuong Vy 2015-05-21 1:49 GMT+09:00 Justin Lemkul jalem...@vt.edu: On 5/20/15 11:55 AM, 姚懿

[gmx-users] Re generate a tpr file

i'm trying to use the following command echo 0|trjconv -f dppc128_1.xtc -s dppc128_1.tpr -o dppc128_1-ini.gro -dump 10 but it appears the following error reading tpx file (dppc128_1.tpr) version 100 with version 83 program. I'm doing Martinez Seara tutorial and in the article uses 4.0.2 gromacs

Re: [gmx-users] About Tabulated Potentials

Dear Justin, Thank you for your reply. When I choose l-J form potential for the non-bonded interactions between CH4 and CH4 using the parameters from another paper, I can get system pressure (25.5Mpa) in accord with experimental value at same conditions. However, when I used tabulated

[gmx-users] Version 100 with version 83 program

I' m running Martínez Seara dppc tutorial and when i use echo 0|trjconv -f dppc128_1.xtc -s dppc128_1.tpr -o dppc128_1-ini.gro -dump 10 it appears the following error: Fatal error: reading tpx file (dppc128_1.tpr) version 100 with version 83 program. I' m using Gromacs 4.6.5 maybe it has

Re: [gmx-users] build nuance in gmx5 (avoiding file INSTALL cannot find gmx)

Chris, On Thu, May 21, 2015 at 5:50 PM, Christopher Neale chris.ne...@alum.utoronto.ca wrote: Dear Szilárd: I report it only because it is allowed in gmx4 builds (or at least it works, I am not sure whether or not is it allowed). By now allowed I meant that things will likely break if you

[gmx-users] Fatal error tpx file

I' m running Martínez Seara dppc tutorial and when i use echo 0|trjconv -f dppc128_1.xtc -s dppc128_1.tpr -o dppc128_1-ini.gro -dump 10 it appears the following error: Fatal error: reading tpx file (dppc128_1.tpr) version 100 with version 83 program. I' m using Gromacs 4.6.5 maybe it

Re: [gmx-users] build nuance in gmx5 (avoiding file INSTALL cannot find gmx)

Dear Szilárd: I report it only because it is allowed in gmx4 builds (or at least it works, I am not sure whether or not is it allowed). I move the source because I often have many modified source trees that I rename to keep things straight. The quick and dirty method that you cite presumes

[gmx-users] Segmentation fault (core dumped) version 4.6.*

Dear gmx users, In order to run my simulations, i usually used the 5.0.* version of gromacs without problems, but since i want to performed umbrella sampling simulations (and since the option pull_geometry=position is not available for the latest versions) For that, i installed the 4.6.7

Re: [gmx-users] Segmentation fault (core dumped) version 4.6.*

Dear Carlos: Are you using a .top file from gromacs 5 with your gromacs 4 runs? If so, try regenerating your topology (and .itp files) using gromacs 4 (with GMXLIB set correctly). Not sure if that would even cause a problem, but it seems like it probably would and is the only thing that comes