Thanks a lot for your insight. I will redefine them.
*Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* *Contact: +91 8898486877* On Mon, May 30, 2016 at 8:26 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 5/30/16 10:55 AM, Anurag Dobhal wrote: > >> Thanks a lot for your reply. >> >> I have set tc-groups as >> >> >> tc-grps = Other acetone ; two coupling groups - more accurate >> tau_t = 0.1 0.1 ; time constant, in ps >> ref_t = 300 300 ; reference temperature, one for each >> >> >> > Then you can't rely on such groups to be correct. Other and acetone > overlap. Define appropriate groups. > > -Justin > > >> >> *Anurag Dobhal* >> *Graduate Student (Bioprocess Technology)* >> *Institute of Chemical Technology, Mumbai* >> *Contact: +91 8898486877* >> >> >> >> On Mon, May 30, 2016 at 8:18 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 5/30/16 10:40 AM, Anurag Dobhal wrote: >>> >>> Dear Gromacs users >>>> >>>> I am solvating my molecule ( a ploymer chain, having 78 atoms) in >>>> Propan-2-one >>>> [ molecules] = acetone. I have already updated [ molecules ] section in >>>> the topology file (topol.top) after the solvation step. >>>> >>>> after the sucessful energy minimization step, while runing grompp I am >>>> geting an error, >>>> >>>> " Excluding 3 bonded neighbours molecule type 'Other' >>>> turning all bonds into constraints... >>>> Excluding 3 bonded neighbours molecule type 'acetone' >>>> turning all bonds into constraints... >>>> Setting gen_seed to 3080450167 >>>> Velocities were taken from a Maxwell distribution at 300 K >>>> Removing all charge groups because cutoff-scheme=Verlet >>>> >>>> Fatal error: >>>> Atom 79 in multiple T-Coupling groups (1 and 2) " >>>> >>>> The error means that T-coupling is treating both the polymer (other) and >>>> solvent (acetone) as other molecules. >>>> How can I rectify the error ? >>>> >>>> >>>> You haven't shown us what you've set as tc-grps but there is clearly >>> redundancy between whatever those groups are. If you have multiple >>> groups, >>> you need to ensure that they are defined correctly, using index groups as >>> needed. >>> >>> -Justin >>> >>> -- >>> ================================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 629 >>> University of Maryland, Baltimore >>> 20 Penn St. >>> Baltimore, MD 21201 >>> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>> http://mackerell.umaryland.edu/~jalemkul >>> >>> ================================================== >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>> posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-requ...@gromacs.org. >>> >>> >> > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.