Re: [gmx-users] grommp warning

2012-08-15 Thread rama david
Thank you Mark for reply. as you said ... Depends whether rigidity or scaling make more sense in your model of real physics, which depends what's in your system. My system is generally consist of proteins or peptides ( single , double or many).. I am using option com Is it right As per

Re: [gmx-users] grommp warning

2012-08-15 Thread Mark Abraham
On 15/08/2012 4:52 PM, rama david wrote: Thank you Mark for reply. as you said ... Depends whether rigidity or scaling make more sense in your model of real physics, which depends what's in your system. My system is generally consist of proteins or peptides ( single , double or many).. I am

Re: [gmx-users] grommp warning

2012-08-14 Thread rama david
Dear shima and Justin, These error is come on Gromacs 4.5.5 at the time of NPT if refcoord_scaling option not used.. But it is not come on Gromacs 4.5.4 when you not use refcoord_scaling option at npt Is any one else has same experience? I really surprised by my observation With

Re: [gmx-users] grommp warning

2012-08-14 Thread Justin Lemkul
On 8/14/12 11:15 AM, rama david wrote: Dear shima and Justin, These error is come on Gromacs 4.5.5 at the time of NPT if refcoord_scaling option not used.. But it is not come on Gromacs 4.5.4 when you not use refcoord_scaling option at npt Is any one else has same experience? I really

Re: [gmx-users] grommp warning

2012-08-14 Thread rama david
Justin, Thank you for your reply, I check the manual but it is giving only small information.. I would be greatly thankfull to you if you shed some light on these option ... With best wishes and regards Rama David -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] grommp warning

2012-08-14 Thread Justin Lemkul
On 8/14/12 11:28 AM, rama david wrote: Justin, Thank you for your reply, I check the manual but it is giving only small information.. I would be greatly thankfull to you if you shed some light on these option ... A simple search of the list archive turns up lots of discussions like

Re: [gmx-users] grommp warning

2012-08-14 Thread rama david
Hi Justin , Thank you for immediate reply and providing the link. But I am wonder for following things... For protein simulation in your lysozyme tutorial we use refcoord_scaling = com In lipid tutorial also same one.. So Is there are any case when to use refcoord_scaling no or all .??

Re: [gmx-users] grommp warning

2012-08-14 Thread Mark Abraham
On 15/08/2012 2:43 PM, rama david wrote: Hi Justin , Thank you for immediate reply and providing the link. But I am wonder for following things... For protein simulation in your lysozyme tutorial we use refcoord_scaling = com In lipid tutorial also same one.. So Is there are any case when to

[gmx-users] grommp warning

2012-08-13 Thread Shima Arasteh
Dear gmx users, I'm simulating a system of protein and water. In NPT equilibration step, I get the error of too many warnings. Anybody knows about this warning? The warning is : WARNING 1 [file NPT.mdp]:   You are using pressure coupling with absolute position restraints, this   will give

[gmx-users] grommp warning

2012-08-13 Thread Shima Arasteh
Dear gmx users, I'm simulating a system of protein and water. In NPT equilibration step, I get the error of too many warnings. Anybody knows about this warning? The warning is : WARNING 1 [file NPT.mdp]:   You are using pressure coupling with absolute position restraints, this   will give

Re: [gmx-users] grommp warning

2012-08-13 Thread Justin Lemkul
On 8/13/12 12:36 PM, Shima Arasteh wrote: Dear gmx users, I'm simulating a system of protein and water. In NPT equilibration step, I get the error of too many warnings. Anybody knows about this warning? Yes, and there are several posts in the list archive explaining its origin,

Re: [gmx-users] grommp warning

2012-08-13 Thread Shima Arasteh
:-) Sincerely, Shima From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, August 14, 2012 12:08 AM Subject: Re: [gmx-users] grommp warning On 8/13/12 12:36 PM

Re: [gmx-users] grommp warning

2012-08-13 Thread Justin Lemkul
On 8/13/12 3:47 PM, Shima Arasteh wrote: OK, thanks. But please let me know something: Is the pressure coupling with absolute position restraints is an option to fix a volume significantly? If yes, then It's me to think about keeping fix the volume of my system or not. You can't have