[gmx-users] Invalid order for directive bondtypes

2013-11-26 Thread Elham Gholamrezai
Dear all I am working on simulation of hydrogen adsorption on graphene sheet, and I need to adopte my force field parameters, new force field folder is made and put in top directory of gromacs. For this reason, I modified charmm27.ff and included new files (bond.itp, nonbond.itp, n2t,

[gmx-users] (no subject)

2013-11-26 Thread Mahboobeh Eslami
hi Dear Gmx Users  i want to study the changing of velocity  in production stage, do i set gen_vel= yes, gen_temp   = 300 and gen_seed   = -1  in all mdp file for Equilibration and production or only in production stage? should I setother options  in the mdp file. Thanks a lot -- Gromacs Users

Re: [gmx-users] Invalid order for directive bondtypes

2013-11-26 Thread Mark Abraham
You're including that file from somewhere that violates the rules in chapter 5. But only you know where. Mark On Nov 26, 2013 11:07 AM, Elham Gholamrezai elham.gholamre...@yahoo.com wrote: Dear all I am working on simulation of hydrogen adsorption on graphene sheet, and I need to adopte my

Re: [gmx-users] energy group tables

2013-11-26 Thread Mark Abraham
Try it! You surely have a test run that will show that your tables work, before you launch into production work, right? :-) On Nov 26, 2013 5:16 AM, Chandan Choudhury iitd...@gmail.com wrote: On Mon, Nov 25, 2013 at 11:22 PM, Humberto Saint-Martin xibas...@gmail.comwrote: Hi, Chandan,

[gmx-users] About g_potential

2013-11-26 Thread Guangwei Jiang
Dear all, Can anyone tell me about the difference when choosing different slice numbers for g_potential function? Thanks very much! Best wishes, Guangwei Jiang -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

Re: [gmx-users] Coulombic potential modifiers in Gromacs 4.6.4.

2013-11-26 Thread Mark Abraham
On Nov 22, 2013 5:58 PM, rajat desikan rajatdesi...@gmail.com wrote: Hi Mark, Thanks for the answer. I have a few doubts. 1) The whole potential is shifted by the value that it would otherwise have had at the cut-off. Doesn't this reduce the well-depth/epsilon for the LJ potential (same

Re: [gmx-users] GPU g_energy problem

2013-11-26 Thread Justin Lemkul
On Mon, Nov 25, 2013 at 3:40 AM, Andrei Neamtu neamtuand...@gmail.comwrote: Dear GMX users, I am simulating a system of two proteins in TIP4P water box. The simulations are performed on a system with 3 servers each containing 16 CPU cores and 2 Tesla 2090 GPU. The problem thai I encounter

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 115, Issue 117

2013-11-26 Thread Justin Lemkul
On Tue, Nov 26, 2013 at 8:08 AM, sunita gupta sunita@gmail.com wrote: Thanks Justin, Its strange that some atomtypes like ha, h1, n2 etc whose parameters are already present in the gbsa.itp are also not recognised. I have many more ligands to deal with. Can you tell me how to overcome

[gmx-users] planned power outage

2013-11-26 Thread Mark Abraham
Hi GROMACS users and devs, There's a planned power outage tomorrow (November 27) to the machine room that houses most of the GROMACS infrastructure. This will mean a period of unavailability of everything except the FTP server and perhaps the mailing lists. We expect no problems, and will bring

[gmx-users] The 20 subsystems are not compatible (REMD)

2013-11-26 Thread Pacho Ramos
Hello I am having a lot of problems to get a REMD simulation end, after running for some time, some replicas are interrupted without writting a state file, leading then to: The 20 subsystems are not compatible error on next run. I have run gmxcheck -f with all state files and I found that the

Re: [gmx-users] The 20 subsystems are not compatible (REMD)

2013-11-26 Thread Mark Abraham
On Tue, Nov 26, 2013 at 2:53 PM, Pacho Ramos pachora...@gmail.com wrote: Hello I am having a lot of problems to get a REMD simulation end, after running for some time, some replicas are interrupted without writting a state file, leading then to: The 20 subsystems are not compatible error

Re: [gmx-users] the changing of velocity in production stage

2013-11-26 Thread Mark Abraham
On Tue, Nov 26, 2013 at 2:47 PM, Mahboobeh Eslami mahboobeh.esl...@yahoo.com wrote: dear mark I am very sorry. I did not understand your answer. please give a clearer answer. 1)do i set gen_vel= yes, gen_temp = 300 and gen_seed = -1 in all mdp file for Equilibration and production

Re: [gmx-users] energy group tables

2013-11-26 Thread Humberto Saint-Martin
The order is irrelevant, except that the tables should be consistent; the way you wrote it: energygrp_table = A A B B C C A B A C B C implies 6 interactions, thus 6 tables: table_A_A.xvg table_B_B.xvg table_C_C.xvg table_A_B.xvg (NOT table_B_A.xvg) table_A_C.xvg (NOT table_C_A.xvg)

Re: [gmx-users] The 20 subsystems are not compatible (REMD)

2013-11-26 Thread Pacho Ramos
2013/11/26 Mark Abraham mark.j.abra...@gmail.com The combination of the current and _prev checkpoint files is supposed to guarantee the existence of a set of .cpt files whose time stamp matches. This should permit you to back up all your files, rename some files appropriately and move on.

Re: [gmx-users] Martini and Gromacs 3 and 4

2013-11-26 Thread Steve
Hi Tsjerk Thanks for you response. Yes, that is exactly what I was confused about. I am presently attempting to use initram.sh. However, I keep getting the following error : Now executing... ./initram.sh -f confout.gro -p systemFG.top Checking dependencies: backward.py ...

Re: [gmx-users] # of threads different than # of cores - gmx hangs.

2013-11-26 Thread Mark Abraham
OK, thanks. We would like to fix that so that it does not hang, but we might need to know some more details. So far, I have failed to replicate your symptoms using 30 threads across 2 nodes with 32 total cores. However, my mpirun and/or OpenMP library was setting thread affinities for me. That may

Re: [gmx-users] Martini and Gromacs 3 and 4

2013-11-26 Thread Tsjerk Wassenaar
Hi Steve, Try using -to gromos The definitions are not (yet) explicitly set for each flavour of gromos. Cheers, Tsjerk On Tue, Nov 26, 2013 at 6:01 PM, Steve steve...@ymail.com wrote: Hi Tsjerk Thanks for you response. Yes, that is exactly what I was confused about. I am presently

Re: [gmx-users] About g_potential

2013-11-26 Thread Andrew DeYoung
Hi Guangwei, The simulation box is binned, or sliced, along z in planes parallel to the xy plane. A greater number of slices means the box is sliced finer -- the bins or slices are smaller. The charges are binned (like making a histogram) into those slices, and the potential is calculated by

[gmx-users] Mailing list archive

2013-11-26 Thread Andrew DeYoung
Hi, Does anyone know if the gmx-users Archive has been moved or is temporarily down? When I do to: http://lists.gromacs.org/pipermail/gmx-users/ it redirects me to: https://mailman-1.sys.kth.se/pipermail/gmx-users/ but that page says, The requested URL /pipermail/gmx-users/ was not found on

Re: [gmx-users] Mailing list archive

2013-11-26 Thread Andrew DeYoung
Hi again, I just realized that Mark sent out an email earlier today announcing a power outage for most of the Gromacs infrastructure, starting at midnight. I think it is almost midnight in Stockholm right now, so probably the outage has started and that's why I'm not able to access

[gmx-users] step 0Segmentation fault: 11

2013-11-26 Thread Valentina
Hello, This problem seems to be quite common, but I still cannot solve it. I am getting following run for mdrun starting mdrun 'System' 100 steps, 0.0 ps. step 0Segmentation fault: 11 If I look at md.log (full file at the end) Grid: 3 x 3 x 2 cells Energies (kJ/mol) Tab. Bonds

Re: [gmx-users] Mailing list archive

2013-11-26 Thread jkrieger
There was a message that the server would be down from midnight to 18:00 GMT+1 On 26 Nov 2013, at 21:08, Andrew DeYoung adeyo...@andrew.cmu.edu wrote: Hi, Does anyone know if the gmx-users Archive has been moved or is temporarily down? When I do to:

[gmx-users] AMBER ff10 with Gromacs

2013-11-26 Thread gromacs query
Dear All I never used Gromacs for nucleic acids. In AMBER there is ff10 (ff99SB+parmbasco+ also one needs to add ions according to water used by Thomas Cheatham et al.) does gromacs include this force field (AMBER ff implemented in gromacs)? regards JIo -- Gromacs Users mailing list * Please

[gmx-users] flags for internal coordinates restraints

2013-11-26 Thread gromacs query
Dear All I want to simulate two polymer chains as rigid bodies, in other words allowing two polymer to interact with each other but keeping their internal coordinates restrained. Also it can be seen as two rods interacting with each other. Which flags/options can be used in Gromacs? regards