Re: [gmx-users] zero charge model- simulation time

2011-07-28 Thread Justin A. Lemkul
Juliette N. wrote: sorry Justin to get back to you gain. This means I have to set zero charges twice ( after grompp EM and grommp MD), since in grompp_md I am using topology file which sets actual charges again to all atoms. Do atoms charges affect EM configuration ? Anything that affects

Re: Re: [gmx-users] zero charge model- simulation time

2011-07-28 Thread wibke . sudholt
Dear Email Sender, Thank you very much for contacting me! Unfortunately, I am not available in the office at the moment and cannot respond to your email. I will be able to handle your request starting again Thursday, August 4, 2011. For all questions about CloudBroker and the CloudBroker Platfo

Re: [gmx-users] zero charge model- simulation time

2011-07-28 Thread Juliette N.
sorry Justin to get back to you gain. This means I have to set zero charges twice ( after grompp EM and grommp MD), since in grompp_md I am using topology file which sets actual charges again to all atoms. Do atoms charges affect EM configuration ? Regards, On 28 July 2011 17:44, Justin A. Lemkul

Re: [gmx-users] zero charge model- simulation time

2011-07-28 Thread Justin A. Lemkul
Juliette N. wrote: Hello Justin, I am using tpbconv to set zero charges after em and after doing grompp_md. grompp -f *.mdp -c *_em.gro -p *.top -o *_md.tpr tpbconv –s *_md.tpr -o *-ZERO_md.tpr –zeroq mdrun -s *-ZERO_md -o -c -e -x -v Do I need to use tpbconv after grompp_em? (before mdru

Re: [gmx-users] zero charge model- simulation time

2011-07-28 Thread Juliette N.
Hello Justin, I am using tpbconv to set zero charges after em and after doing grompp_md. grompp -f *.mdp -c *_em.gro -p *.top -o *_md.tpr tpbconv –s *_md.tpr -o *-ZERO_md.tpr –zeroq mdrun -s *-ZERO_md -o -c -e -x -v Do I need to use tpbconv after grompp_em? (before mdrun_em) Regards, On 28 J

Re: [gmx-users] zero charge model- simulation time

2011-07-28 Thread Justin A. Lemkul
Juliette N. wrote: Hi again, I am wondering if using tpbconv to set zero charges (case 1) works similar to when one sets zero atom charges in topology file from the very beginning (case 2). Do these two cases work similarly? They should work identically. I checked tpr file and I see th

Re: [gmx-users] zero charge model- simulation time

2011-07-28 Thread Juliette N.
Hi again, I am wondering if using tpbconv to set zero charges (case 1) works similar to when one sets zero atom charges in topology file from the very beginning (case 2). Do these two cases work similarly? I checked tpr file and I see that charges are set to zero. Can you please tell me what the

Re: [gmx-users] zero charge model- simulation time

2011-07-28 Thread Justin A. Lemkul
Juliette N. wrote: Thanks Justin. One last question, I wanted to make sure if zetting zero charge using tpbconv is identical to setting zero charges in top file. Yes. Verify the contents of your .tpr file with gmxdump. I am concerned about the model to be inaccurate. Do these two models

Re: [gmx-users] zero charge model- simulation time

2011-07-28 Thread Juliette N.
Thanks Justin. One last question, I wanted to make sure if zetting zero charge using tpbconv is identical to setting zero charges in top file. I am concerned about the model to be inaccurate. Do these two models work similarly? Regards, On 28 July 2011 12:54, Justin A. Lemkul wrote: > > > Juli

Re: [gmx-users] zero charge model- simulation time

2011-07-28 Thread Justin A. Lemkul
Juliette N. wrote: Hello, I set zero charges to all atoms using the commands below: grompp -f *.mdp -c *_em.gro -p *.top -o *_md.tpr tpbconv –s *_md.tpr -o *-ZERO_md.tpr –zeroq mdrun -s *-ZERO_md -o -c -e -x -v So before doing mdrun md I add tpbconv command and use the out put *-ZERO_md.