[gmx-users] grompp error : Atomtype CAro not found
Hi Dallas, thanks for your answer. I saw README file in gromos54a7_atb.ff from ATB server. My system contains lipid molecules and small molecule. For lipid molecules, Justine Lemkul suggested to use gromos53a6_lipid.ff. How to use both of gromos54a7_atb.ff and gromos53a6_lipid.ff in topology file. Please guide me. Best, Atila -- 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.
Re: [gmx-users] install and mdrun problems
Sounds bit like it may be overheating. Are all ventilation fans fully operational? On Mon, 2 Mar. 2020, 2:38 pm Bogdanov, Vladimir, wrote: > Hi all, > > I installed Gromacs2020 on ubuntu18.04 (nvidia-smi 440.59, CUDA 10.2), but > when I did make check, my PC turned off. I also tried to install > Gromacs2018.2, Gromacs2018.6 and I have got the same problem. When I tried > to do mdrun, my PC also shut down. I also tried the following combination: > nvidia-smi 440.59, CUDA 9.2. > > Any ideas would be helpful. > > Thanks, > Vlad > -- > 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. > -- 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.
[gmx-users] install and mdrun problems
Hi all, I installed Gromacs2020 on ubuntu18.04 (nvidia-smi 440.59, CUDA 10.2), but when I did make check, my PC turned off. I also tried to install Gromacs2018.2, Gromacs2018.6 and I have got the same problem. When I tried to do mdrun, my PC also shut down. I also tried the following combination: nvidia-smi 440.59, CUDA 9.2. Any ideas would be helpful. Thanks, Vlad -- 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.
[gmx-users] PC turned off after starting minimization
Hi all, I have installed -- 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.
Re: [gmx-users] grompp error : Atomtype CAro not found
Did you read what the ATB told you about the topologies it generates, and what forcefield you have to use? There is a warning posted on the page where you download your topology files that applies directly to this error you have encountered: "*Warning!* This molecule contains non-standard atom types not included in the standard GROMOS 54A7 forcefield. To use these atom types the internal GROMACS parameter files must be updated. These can be downloaded using the link below. Instructions on where to place (and how to use) the files are provided in the README file included in the archive." ATB uses GROMOS 54a7 ATB, and you have to download and use that forcefield for any molecules you generate using that server. You cannot just mix it with GROMOS 53a6 like you have tried to, since 54a7_atb has additional atom types. Stick with a single forcefield, do not mix then because the vast majority are not compatible in that manner. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Sun, 1 Mar 2020 at 19:41, Atila Petrosian wrote: > Hi gromacs users, > > I am doing MD simulation of my system (DPPC lipid + 2 drug molecules + > water molecules) using gromacs 2019. > > I used ATB for drug molecules and Membrane Protein: KALP15 in DPPC > gromacs tutorial method for lipid molecules (based on Justin Lemkul > suggestion in my previous post: > > https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2020-February/128420.html > ). > > --- > My topology file is as follows: > --- > ; Include forcefield parameters > #include "gromos53a6_lipid.ff/forcefield.itp" > > ; Include Position restraint file > #ifdef POSRES > #include "posre.itp" > #endif > > ; Include DPPC chain topology > #include "dppc.itp" > > ; Include drug topology > #include "lig.itp" > > ; Include water topology > #include "gromos53a6_lipid.ff/spc.itp" > > #ifdef POSRES_WATER > ; Position restraint for each water oxygen > [ position_restraints ] > ; i funct fcxfcyfcz >11 1000 1000 1000 > #endif > > [ system ] > ; Name > dopc/lig/sol in water > > [ molecules ] > ; Compound#mols > DPPC 128 > LIG 2 > SOL 8257 > --- > My lig.itp file is as follows: > --- > . > . > ; > [ moleculetype ] > ; Name nrexcl > LIG 3 > > [ atoms ] > ; nr type resnr resid atom cgnr chargemass > 1HC1LIGH2710.131 1.0080 > 2 CAro1LIGC242 -0.130 12.0110 > 3 CAro1LIGC233 -0.130 12.0110 > 4HC1LIGH2640.131 1.0080 > 5 CAro1LIGC225 -0.119 12.0110 > 6HC1LIGH2560.135 1.0080 > 7 CAro1LIGC217 -0.039 12.0110 > 8 CAro1LIGC268 -0.119 12.0110 > 9HC1LIGH2990.135 1.0080 >10 CAro1LIGC25 10 -0.130 12.0110 >11HC1LIGH28 110.131 1.0080 >12 C1LIGC18 12 -0.051 12.0110 >13 CH21LIGC19 130.055 14.0270 >14 CH31LIGC20 140.020 15.0350 >15 CAro1LIGC11 15 -0.025 12.0110 >16 CAro1LIGC12 16 -0.040 12.0110 >17 CAro1LIGC13 17 -0.117 12.0110 >18HC1LIGH15 180.137 1.0080 >19 CAro1LIGC14 19 -0.133 12.0110 >20HC1LIGH16 200.131 1.0080 >21 CAro1LIGC15 21 -0.129 12.0110 >22HC1LIGH17 220.131 1.0080 >23 CAro1LIGC16 23 -0.133 12.0110 >24HC1LIGH18 240.131 1.0080 >25 CAro1LIGC17 25 -0.117 12.0110 >26HC1LIGH19 260.137 1.0080 >27 CAro1LIG C8 27 -0.076 12.0110 >28 CAro1LIG C7 28 -0.079 12.0110 >29HC1LIGH12 290.139 1.0080 >30 CAro1LIG C6 30 -0.184 12.0110 >31HC1LIGH11 310.143 1.0080 >32 CAro1LIG C5 320.087 12.0110 >33 CAro1LIGC10 33 -0.184 12.0110 >34HC1LIGH14 340.143 1.0080 >35 CAro1LIG C9 35 -0.079 12.0110 >36HC1LIGH13 360.139 1.0080 >37OE1LIG O1 37 -0.219 15.9994 >38 CH21LIG C4 380.149 14.0270 >39 CH21LIG C3 390.101 14.0270 >40 NTer1LIG N1 40 -0.267 14.0067
Re: [gmx-users] Collision
This all sounds like http://manual.gromacs.org/documentation/current/user-guide/terminology.html#gmx-pbc Remember, the box is just a visualisation of what the system looks like, and you can move that box anywhere. What is in the center of the box is entirely up to you and the post processing you do. What comes out of the mdrun engine is arbitrary. With VMD, and I suspect the other MD visualisation software such as pymol, you can turn on the periodic images. Have you done that to see where things are actually located? What did you see? Have you actually processed it using trjconv to put it back in the center of the box to see what is actually going on? What command did you use, and how did it then look? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Sat, 29 Feb 2020 at 09:15, Mohamed Abdelaal wrote: > Hello all, > > I created a graphene sheet and performed energy minimization, after energy > minimization I found that parts of the graphene sheet was moved from the > box bottom to the box topside at the same place (as if it was translated > upwards). I looked online for the problem and I understood that I should > restrain the graphene sheet along the z axis. I did that using force =1000. > and the problem was solved and nothing moved. > > After that I tried to insert 25 molecule of (C60) inside a box which > contains the graphene sheet. I did that and did the energy minimization but > part of the graphene sheet moved again from its place although the maximum > force was less than 1000 which is the force I used to restrain the graphene > sheet. However I didn't have any error during the energy minimization. Does > this means that the problem is just in visualization or I might have a > problem in my energy minimization ? > > It is also worth mentioning that the C60 molecules are not spherical as it > should be. I read about that and I found people mentioning that this shape > deformation in only a visualization problem and can be solved by using gmx > trjconv. is it possible that this problem has happened to my whole system > including the graphene sheet or it shouldn't affect my graphene sheet as > long as I have restrained it ? > > more info: > I used periodic_molecules = yes while trying to minimize my whole system. > (I also tried without it but no impact) > I wrote: > > gmx grompp -f minim.mdp -c C60_GRM_box.gro -r C60_GRM_box.gro -p > C60_GRM_box.top -o min1.tpr -maxwarn 2 > > followed by > gmx mdrun -v -deffnm min1 > > and I got the below result: > writing lowest energy coordinates. > > Steepest Descents converged to Fmax < 1000 in 3293 steps > Potential Energy = 6.3598562e+05 > Maximum force = 9.9486487e+02 on atom 12087 > Norm of force = 6.5454323e+01 > > Can anybody help me please. > > Thanks > > Mohamed > -- > 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. > -- 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.
[gmx-users] grompp error : Atomtype CAro not found
Hi gromacs users, I am doing MD simulation of my system (DPPC lipid + 2 drug molecules + water molecules) using gromacs 2019. I used ATB for drug molecules and Membrane Protein: KALP15 in DPPC gromacs tutorial method for lipid molecules (based on Justin Lemkul suggestion in my previous post: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2020-February/128420.html ). --- My topology file is as follows: --- ; Include forcefield parameters #include "gromos53a6_lipid.ff/forcefield.itp" ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Include DPPC chain topology #include "dppc.itp" ; Include drug topology #include "lig.itp" ; Include water topology #include "gromos53a6_lipid.ff/spc.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif [ system ] ; Name dopc/lig/sol in water [ molecules ] ; Compound#mols DPPC 128 LIG 2 SOL 8257 --- My lig.itp file is as follows: --- . . ; [ moleculetype ] ; Name nrexcl LIG 3 [ atoms ] ; nr type resnr resid atom cgnr chargemass 1HC1LIGH2710.131 1.0080 2 CAro1LIGC242 -0.130 12.0110 3 CAro1LIGC233 -0.130 12.0110 4HC1LIGH2640.131 1.0080 5 CAro1LIGC225 -0.119 12.0110 6HC1LIGH2560.135 1.0080 7 CAro1LIGC217 -0.039 12.0110 8 CAro1LIGC268 -0.119 12.0110 9HC1LIGH2990.135 1.0080 10 CAro1LIGC25 10 -0.130 12.0110 11HC1LIGH28 110.131 1.0080 12 C1LIGC18 12 -0.051 12.0110 13 CH21LIGC19 130.055 14.0270 14 CH31LIGC20 140.020 15.0350 15 CAro1LIGC11 15 -0.025 12.0110 16 CAro1LIGC12 16 -0.040 12.0110 17 CAro1LIGC13 17 -0.117 12.0110 18HC1LIGH15 180.137 1.0080 19 CAro1LIGC14 19 -0.133 12.0110 20HC1LIGH16 200.131 1.0080 21 CAro1LIGC15 21 -0.129 12.0110 22HC1LIGH17 220.131 1.0080 23 CAro1LIGC16 23 -0.133 12.0110 24HC1LIGH18 240.131 1.0080 25 CAro1LIGC17 25 -0.117 12.0110 26HC1LIGH19 260.137 1.0080 27 CAro1LIG C8 27 -0.076 12.0110 28 CAro1LIG C7 28 -0.079 12.0110 29HC1LIGH12 290.139 1.0080 30 CAro1LIG C6 30 -0.184 12.0110 31HC1LIGH11 310.143 1.0080 32 CAro1LIG C5 320.087 12.0110 33 CAro1LIGC10 33 -0.184 12.0110 34HC1LIGH14 340.143 1.0080 35 CAro1LIG C9 35 -0.079 12.0110 36HC1LIGH13 360.139 1.0080 37OE1LIG O1 37 -0.219 15.9994 38 CH21LIG C4 380.149 14.0270 39 CH21LIG C3 390.101 14.0270 40 NTer1LIG N1 40 -0.267 14.0067 41 CH31LIG C1 410.097 15.0350 42 CH31LIG C2 420.097 15.0350 ; total charge of the molecule: 0.000 [ bonds ] ; ai aj funct c0 c1 122 0.1090 1.2300e+07 232 0.1390 8.6600e+06 . . . --- After using command: gmx grompp -f em1.mdp -c system.gro -p topol.top -o em1.tpr, I encountered with the following error: --- ERROR 1 [file lig.itp, line 66]: Atomtype CAro not found --- How to resole it? Best, Atila -- 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.
