Re: [gmx-users] Tools for energy of solvation in polimers

On 11/9/15 8:33 AM, Mishelle Oña wrote: Hi, Yes I remember. However I only found that MM/PBSA could be done only with NAMD. Is it posible to make it in gromacs? Could you explain me a little bit how it works o any helpfull link?Mishelle Google knows all about it. There's a program and

Re: [gmx-users] periodic molecule

Thanks a lot. Regards, Pierre On 09/11/15 11:54, CHEN Pan wrote: To set up an infinite cellulose chain, you need: 1): Set up" periodic_molecules = yes" in your mdp file. 2): Built the connection, such as bonds, angles, dihedrals and 1-4 pairs between the last residue and the first residue in

Re: [gmx-users] mpirun

On 11/9/15 5:23 AM, Said wrote: Hi, I have a gateway access to uppmax. I could have copied 1aki.pdb to my account using box.com since scp does not work. when writing mpirun -np 1 pdb2gmx -f 1aki.pdb -o 1aki_processed.gro -water spce, it gives me an error with exit code: 225. There is not

Re: [gmx-users] Tools for energy of solvation in polimers

Hi, Yes I remember. However I only found that MM/PBSA could be done only with NAMD. Is it posible to make it in gromacs? Could you explain me a little bit how it works o any helpfull link?Mishelle > To: gmx-us...@gromacs.org > From: jalem...@vt.edu > Date: Mon, 9 Nov 2015 08:30:06 -0500 >

Re: [gmx-users] Tools for energy of solvation in polimers

On 11/9/15 8:18 AM, Mishelle Oña wrote: OK I understand, so you think I couldn´t use Gromacs to calculate the Energy of Solvation? If that is the case could you help me with a tutorial or other tipe of information that could help me with this staff. Please I have been struggling with this

[gmx-users] Tools for energy of solvation in polimers

OK I understand, so you think I couldn´t use Gromacs to calculate the Energy of Solvation? If that is the case could you help me with a tutorial or other tipe of information that could help me with this staff. Please I have been struggling with this for weeks. I need to solve it Mishelle >

Re: [gmx-users] mpirun

Hi Justin, Is gmx the same as ngmx? Here are the binaries in the Uppmax gromacs directory: [samuelf@tintin1 ~]$ ls /sw/apps/gromacs/4.6.3/tintin/bin/ GMXRCg_anadock_d g_cluster g_densorder_d g_enemat g_helixorient_d g_morph g_pme_error_d g_rmsdistg_select_d

[gmx-users] DPPC hlothane Residue DPP not found in residue topology database

Hello: Concerning about my last question of DPPC membrane and halothane simulation and the GROMOS 53a6. When i used pdb2gmx the following error appears: Residue DPP not found in residue topology database. Then, i googled to Gromacs webpage and i found

Re: [gmx-users] DPPC hlothane Residue DPP not found in residue topology database

On 11/9/15 1:11 PM, Poncho Arvayo Zatarain wrote: Hello: Concerning about my last question of DPPC membrane and halothane simulation and the GROMOS 53a6. When i used pdb2gmx the following error appears: Residue DPP not found in residue topology database. Then, i googled to Gromacs webpage

Re: [gmx-users] mpirun

Thank you! On Mon, Nov 9, 2015 at 8:18 PM, Samuel Flores wrote: > Oh that makes sense! > > Elsaid, issue: > > module load gromacs/5.0.4 > > "module load gromacs" defaults to an ancient release of gromacs. > > Sam > > > On Nov 9, 2015, at 19:10, Justin Lemkul

Re: [gmx-users] mpirun

On 11/9/15 1:08 PM, Samuel Flores wrote: Hi Justin, Is gmx the same as ngmx? Here are the binaries in the Uppmax gromacs directory: gmx refers to the single binary provided as of 5.0, which is the new setup. What appears here is a (very) outdated version of GROMACS, and usage needs to be

Re: [gmx-users] mpirun

Oh that makes sense! Elsaid, issue: module load gromacs/5.0.4 "module load gromacs" defaults to an ancient release of gromacs. Sam > On Nov 9, 2015, at 19:10, Justin Lemkul wrote: > > > > On 11/9/15 1:08 PM, Samuel Flores wrote: >> Hi Justin, >> >> Is gmx the same as

Re: [gmx-users] Problem with Charges

On 11/9/15 12:04 PM, faride badalkhani wrote: Dear all, I have parameterized a relatively large molecule (136 atom) with PRODRG server, and then I assigned charges and charge groups in a building bock style manner. I know that my system include a total +8 charge, but when I execute genbox

[gmx-users] GROMACS 5.1.1 official release

Hi GROMACS users, The official release of GROMACS 5.1.1 is available! This release fixes some known bugs in 5.1, incorporates all fixes made in the recent 5.0.7 release, and makes minor enhancements for forward-compatibility for upcoming CUDA versions. We encourage all users of 5.1 to update to

[gmx-users] per atom stress tensor from g_energy

Dear all, I want to calculate the thermal conductivity of small molecules. I can see that I need heat current, J. J has a term Si which is the per atom stress tensor according to JPC, 141, 134101. Does anybody know how I can extract this term from the simulation with g_energy or any other tool.

Re: [gmx-users] mpirun

Hi, Thank you for your response. When writing gmx, it gives the command not found. (Note I use windows) Elsaid On Mon, Nov 9, 2015 at 3:31 PM, Justin Lemkul wrote: > > > On 11/9/15 5:23 AM, Said wrote: > >> Hi, >> >> I have a gateway access to uppmax. I could have copied

[gmx-users] Problem with Charges

Dear all, I have parameterized a relatively large molecule (136 atom) with PRODRG server, and then I assigned charges and charge groups in a building bock style manner. I know that my system include a total +8 charge, but when I execute genbox command i receive the following note: System total

Re: [gmx-users] mpirun

On 11/9/15 11:55 AM, Elsaid Younes wrote: Hi, Thank you for your response. When writing gmx, it gives the command not found. (Note I use windows) Then you haven't configured your environment correctly.

[gmx-users] QM/MM

I'm looking to try a QM/MM simulation for a protein-DNA system using Gussian09 & GROMACS 4.6 (these are available at the local cluster). Does anyone has any experience working and getting results in this environment? Are there any notable problems? Should I pay special attention to any

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 139, Issue 34

Hi, All your links give me the following, so I can't see what errors you are getting: 403 Forbidden JSP3/2.0.4 But, you don't have to renumber the atoms in your PDB file. Gromacs ignores those numbers and uses its own numbers. Otherwise, how could it deal

[gmx-users] mpirun

Hi, I have a gateway access to uppmax. I could have copied 1aki.pdb to my account using box.com since scp does not work. when writing mpirun -np 1 pdb2gmx -f 1aki.pdb -o 1aki_processed.gro -water spce, it gives me an error with exit code: 225. Elsaid -- Gromacs Users mailing list * Please

Re: [gmx-users] mpirun

Hi, it gives me file input/output error 1aki.pdb. Elsaid On Mon, Nov 9, 2015 at 8:20 PM, Elsaid Younes wrote: > Thank you! > > On Mon, Nov 9, 2015 at 8:18 PM, Samuel Flores > wrote: > >> Oh that makes sense! >> >> Elsaid, issue: >> >> module load

[gmx-users] periodic molecule

Dear GMX users, I am currently simulating a system involving an infinite slab of cellulose. To model it properly, I need each cellulose chain to be a periodic molecule. I assume the keyword "periodic-molecule" is there to provide such a feature. However, it is not clear from the manual how

[gmx-users] How to build a correct structure file beyond 99999 atoms using pdb or gro extend format ?

Dear, I did some operations on my pdb or gro format file, for example, I deleted some atoms randomly to mimic a hole, then I had to re-number atoms in the pdb or gro format file by my code. The re-new pdb or gro file like picture 1 LINK:

Re: [gmx-users] periodic molecule

To set up an infinite cellulose chain, you need: 1): Set up" periodic_molecules = yes" in your mdp file. 2): Built the connection, such as bonds, angles, dihedrals and 1-4 pairs between the last residue and the first residue in your topology file. Infinite chain usually means the end of molecules

Re: [gmx-users] mpirun

On 11/9/15 7:59 PM, Elsaid Younes wrote: Hi, it gives me file input/output error 1aki.pdb. The most likely explanation is that file doesn't exist in the working directory. -Justin Elsaid On Mon, Nov 9, 2015 at 8:20 PM, Elsaid Younes wrote: Thank you! On Mon, Nov