[gmx-users] T-Coupling groups in NVT

2013-03-21 Thread Shima Arasteh
Hi, I am simulating a system of POPC/Water/Ions/protein. Ions are 1 M NaCL and 3 CL atoms to neutralize the system. In NVT step, I have coupling groups as : tc-grps        = Protein POPC    SOL_CL    comm_grps    = Protein_POPC SOL_CL when I run the grompp for NVT, I get the error that the

Re: [gmx-users] T-Coupling groups in NVT

2013-03-21 Thread Justin Lemkul
On Thu, Mar 21, 2013 at 8:56 AM, Shima Arasteh shima_arasteh2...@yahoo.comwrote: Hi, I am simulating a system of POPC/Water/Ions/protein. Ions are 1 M NaCL and 3 CL atoms to neutralize the system. In NVT step, I have coupling groups as : tc-grps= Protein POPCSOL_CL comm_grps

Re: [gmx-users] T-Coupling groups in NVT

2013-03-21 Thread Gunther Lukat
I general, I have good results with coupling Ions together with the water. Dipl.-Inf. Gunther Lukat g.lu...@gmx.net www.aplvoro.org Am 21.03.2013 um 13:56 schrieb Shima Arasteh shima_arasteh2...@yahoo.com: Hi, I am simulating a system of POPC/Water/Ions/protein. Ions are 1 M NaCL and 3

Re: [gmx-users] T-Coupling groups in NVT

2013-03-21 Thread Shima Arasteh
users gmx-users@gromacs.org Sent: Thursday, March 21, 2013 4:31 PM Subject: Re: [gmx-users] T-Coupling groups in NVT I general, I have good results with coupling Ions together with the water.  Dipl.-Inf. Gunther Lukat g.lu...@gmx.net www.aplvoro.org Am 21.03.2013 um 13:56 schrieb Shima

Re: [gmx-users] T-coupling groups

2010-03-19 Thread Zuzana Benkova
Dear Srinivs,thank you for response. You are right I have already found the source of problem. I have used PEO to name the chain group and forgot that the same group holded for residues. GreetingsZuzanaDňa 03/19/10, jampani srinivas jampa...@gmail.com napísal:Dear Zuzana, Recently i have done

Re: [gmx-users] T-coupling groups

2010-03-18 Thread Justin A. Lemkul
Zuzana Benkova wrote: Dear GROMACS users, I have checked the mails in archive which deal with the problem I am facing but did not find the answer what I do wrong. I want to compile a PEO chain centered in box of 2900 water molecules. In my md.mdp the relevant section is as follows Tcoupl

Re: [gmx-users] T-coupling groups

2010-03-18 Thread jampani srinivas
Dear Zuzana, Recently i have done similar selection, I have got this error only when i miss some atoms or when i have some atoms in both groups. I would suggest you to check your groups carefully or you can make indexes for these selections in VMD and check whether you are missing some atoms from