Re: [gmx-users] Acetonitrile with CHARMM ff

2017-07-13 Thread Justin Lemkul
On 7/13/17 9:16 AM, Sonia Milena Aguilera Segura wrote: Message: 2 Date: Thu, 13 Jul 2017 08:56:14 -0400 From: Justin Lemkul To: Discussion list for GROMACS users Subject: Re: [gmx-users] umbrella sampling Message-ID:

Re: [gmx-users] Acetonitrile with CHARMM ff

2017-07-13 Thread Sonia Milena Aguilera Segura
- Original Message - > From: "gromacs org gmx-users-request" > > To: "gromacs org gmx-users" > Sent: Thursday, July 13, 2017 2:58:39 PM > Subject: gromacs.org_gmx-users Digest, Vol 159,

Re: [gmx-users] Acetonitrile using CHARMM ff

2017-07-11 Thread Justin Lemkul
On 7/10/17 10:52 AM, Sonia Milena Aguilera Segura wrote: Dear Justin, Thank you for the answer. I changed the two parameters suggested in the mdp file and I ran again a minimization, 200 ps NVT, 200 ps NPT, and 1 ns MD for the two cases of the previous mail, and now I am getting densities

Re: [gmx-users] Acetonitrile using CHARMM ff

2017-07-10 Thread Sonia Milena Aguilera Segura
Dear Justin, Thank you for the answer. I changed the two parameters suggested in the mdp file and I ran again a minimization, 200 ps NVT, 200 ps NPT, and 1 ns MD for the two cases of the previous mail, and now I am getting densities around 771 g/m3 which is slightly underestimated, but close

Re: [gmx-users] Acetonitrile with CHARMM ff

2017-07-07 Thread Justin Lemkul
On 7/7/17 10:11 AM, Sonia Milena Aguilera Segura wrote: Dear Justin, Thank you very much for your answer. I tried both approaches: erasing the dihedral from the topology (first approach) and modifying the ffbonded.itp as described in the previous mail, without adding any improper (second

Re: [gmx-users] Acetonitrile with CHARMM ff

2017-07-07 Thread Sonia Milena Aguilera Segura
Dear Justin, Thank you very much for your answer. I tried both approaches: erasing the dihedral from the topology (first approach) and modifying the ffbonded.itp as described in the previous mail, without adding any improper (second approach). I ran a minimization, 200 ps NVT, 200 ps NPT, and

Re: [gmx-users] Acetonitrile with CHARMM ff

2017-07-06 Thread Justin Lemkul
On 7/6/17 6:34 AM, Sonia Milena Aguilera Segura wrote: Dear Justin, Thank you for your reply. I went trough the CHARMM forum and I found this post of 2007, https://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat=28545, which basically underlines the same issues I am having. I read

Re: [gmx-users] Acetonitrile with CHARMM ff

2017-07-06 Thread Sonia Milena Aguilera Segura
Dear Justin, Thank you for your reply. I went trough the CHARMM forum and I found this post of 2007, https://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat=28545, which basically underlines the same issues I am having. I read this post before posting here, and this why I came with the