RE: [gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder
Is the problem specific to cylinder geometry? Do other settings work? Does it make a difference if you set values for pull_r0 and pull_r1? -Justin I would think that it is the cylinder geometry that creates the problem. If I use pull= umbrellapull_geometry = distancepull_dim = N N Ypull_start = yespull_init1 = 0.0pull_ngroups = 1pull_group0 = DPPCpull_group1 = drugpull_rate1= 0.0 The molecules stays in place. But pull_geometry=distance is what I would prefer due to the undulations. Changing pull_r0 and pull_r1 still makes the drug molecule move down towards the membrane... -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] disulfide bonds
I'm trying to work on thrombin pdf file with 2 chains. The pdb code is 1PPB.pdb The main problem is: When I use pdb2gmx it adds H atoms to Cys, hence the disulfide bonds are no longer conected after energy minimization. How can I avoid this addition of H atoms? (I tried to make this bond after, but I didn't make it because one Cys is in the long chain and the other one is in the short chain) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] disulfide bonds
On 29/04/2012 7:02 PM, Hagit G wrote: I'm trying to work on thrombin pdf file with 2 chains. The pdb code is 1PPB.pdb The main problem is: When I use pdb2gmx it adds H atoms to Cys, hence the disulfide bonds are no longer conected after energy minimization. How can I avoid this addition of H atoms? (I tried to make this bond after, but I didn't make it because one Cys is in the long chain and the other one is in the short chain) See http://www.gromacs.org/Documentation/How-tos/Making_Disulfide_Bonds about requirements for having atoms (and thus chains) in the same [moleculetype]. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Make an index file
Actually, I am confused somehow. I want to equilibrate the system. It contains popc and water. To equilibrate it, using .mdp file I use the nvt.mdp file as below. title = NVT equilibration for POPC define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = POPC SOL ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 323 323 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 323 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed I enter this command: # grompp -f nvt.mdp -c em.gro -p popc.top -o nvt.tpr Getting this fatal error: Group POPC not found in index file. Group names must match either [moleculetype] names or custom index group names,in which case you must supply an index file to the '-n' option of grompp. I don't need index file, do I? What is the problem with my .mdp file? Cheers, Shima From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, April 29, 2012 3:10 AM Subject: Re: [gmx-users] Make an index file On 4/28/12 2:06 PM, Peter C. Lai wrote: #2 Generally a good idea to keep the names consistent, however - why are you using POP in the coordinate file instead of POPC? If it is a .pdb file, the standard residue name occupies 3 characters. Many files (including those from Tieleman) are distributed with such names. To the OP's original question - the commands you issue depend on what you're trying to achieve. What group do you need to create? -Justin -- Sent from my Android phone with K-9 Mail. Please excuse my brevity. Shima Arasteh shima_arasteh2...@yahoo.com wrote: Dear gmx users, I want to simulate POPC in water. In equilibration step, I have to make an index file. But when I enter this command, I do not know to choose which group to make a suitable .ndx file which matches the molecule types and molecules sections in .top file . The .top file contains these: [ moleculetype ] ; Name nrexcl POPC 3 . . . . [ system ] ; name POPC in water [ molecules ] ; name number POPC 128 SOL 3800 It is the command I enter: # make_ndx -f em.gro -o index.ndx 0 System : 18056 atoms 1 Other : 6656 atoms 2 POP : 6656 atoms 3 Water : 11400 atoms 4 SOL : 11400 atoms 5 non-Water : 6656 atoms nr : group ! 'name' nr name 'splitch' nr Enter: list groups 'a': atom 'del' nr 'splitres' nr 'l': list residues 't': atom type | 'keep' nr 'splitat' nr 'h': help 'r': residue 'res' nr 'chain' char name: group 'case': case sensitive 'q': save and quit 'ri': residue index Now, what is the correct answer? Anybody can suggest me? Thanks in advance, Shima ge -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin --
Re: [gmx-users] Make an index file
On 29/04/2012 7:32 PM, Shima Arasteh wrote: Actually, I am confused somehow. I want to equilibrate the system. It contains popc and water. To equilibrate it, using .mdp file I use the nvt.mdp file as below. title= NVT equilibration for POPC define= -DPOSRES; position restrain the protein ; Run parameters integrator= md; leap-frog integrator nsteps= 5; 2 * 5 = 100 ps dt= 0.002; 2 fs ; Output control nstxout= 100; save coordinates every 0.2 ps nstvout= 100; save velocities every 0.2 ps nstenergy= 100; save energies every 0.2 ps nstlog= 100; update log file every 0.2 ps ; Bond parameters continuation= no; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cels nstlist= 5; 10 fs rlist= 1.2; short-range neighborlist cutoff (in nm) rcoulomb= 1.2; short-range electrostatic cutoff (in nm) rvdw= 1.2; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps= POPC SOL; two coupling groups - more accurate Here you instruct grompp to expect the POPC group... tau_t= 0.10.1; time constant, in ps ref_t= 323 323; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl= no ; no pressure coupling in NVT ; Periodic boundary conditions pbc= xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel= yes; assign velocities from Maxwell distribution gen_temp= 323; temperature for Maxwell distribution gen_seed= -1; generate a random seed I enter this command: # grompp -f nvt.mdp -c em.gro -p popc.top -o nvt.tpr Getting this fatal error: Group POPC not found in index file. Group names must match either [moleculetype] names or custom index group names,in which case you must supply an index file to the '-n' option of grompp. I don't need index file, do I? What is the problem with my .mdp file? ... but POPC is not defined implicitly by your .top+.gro combination, nor explicitly in an index file supplied with grompp -n. AFAIK if your [moleculetype] is named POPC then it is all OK, but maybe the fact that your .gro file has the POPC residues named POP is confusing that mechanism. As you can see with your earlier example with make_ndx, the POP group is defined implicitly by the residue names in your .gro file, so if you use that output index file and reference POP in your .mdp file, all will be good. You might get away without using that index file, but I am not sure about this. Simpler still is to use Water and non-Water as your T-coupling groups, but this will need changing if down the road you need Protein as well (or such). Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Make an index file
Dear MArkWow, That was kind of you. I appreciate you. Ok, I will try it. Thanks, Shima From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, April 29, 2012 2:11 PM Subject: Re: [gmx-users] Make an index file On 29/04/2012 7:32 PM, Shima Arasteh wrote: Actually, I am confused somehow. I want to equilibrate the system. It contains popc and water. To equilibrate it, using .mdp file I use the nvt.mdp file as below. title = NVT equilibration for POPC define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = POPC SOL ; two coupling groups - more accurate Here you instruct grompp to expect the POPC group... tau_t = 0.1 0.1 ; time constant, in ps ref_t = 323 323 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 323 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed I enter this command: # grompp -f nvt.mdp -c em.gro -p popc.top -o nvt.tpr Getting this fatal error: Group POPC not found in index file. Group names must match either [moleculetype] names or custom index group names,in which case you must supply an index file to the '-n' option of grompp. I don't need index file, do I? What is the problem with my .mdp file? ... but POPC is not defined implicitly by your .top+.gro combination, nor explicitly in an index file supplied with grompp -n. AFAIK if your [moleculetype] is named POPC then it is all OK, but maybe the fact that your .gro file has the POPC residues named POP is confusing that mechanism. As you can see with your earlier example with make_ndx, the POP group is defined implicitly by the residue names in your .gro file, so if you use that output index file and reference POP in your .mdp file, all will be good. You might get away without using that index file, but I am not sure about this. Simpler still is to use Water and non-Water as your T-coupling groups, but this will need changing if down the road you need Protein as well (or such). Mark -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] disulfide bonds
thank you very much That was what I've tried to use pdb2gmx-ss, this is not useful, 'cause it's not in the same unit. My problem is not the distance. Hagit 2012/4/29, Mark Abraham mark.abra...@anu.edu.au: On 29/04/2012 7:02 PM, Hagit G wrote: I'm trying to work on thrombin pdf file with 2 chains. The pdb code is 1PPB.pdb The main problem is: When I use pdb2gmx it adds H atoms to Cys, hence the disulfide bonds are no longer conected after energy minimization. How can I avoid this addition of H atoms? (I tried to make this bond after, but I didn't make it because one Cys is in the long chain and the other one is in the short chain) See http://www.gromacs.org/Documentation/How-tos/Making_Disulfide_Bonds about requirements for having atoms (and thus chains) in the same [moleculetype]. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Make an index file
Dear Mark, Wow, That was kind of you. I appreciate you. Ok, I will try it. Thanks,Shima From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, April 29, 2012 2:11 PM Subject: Re: [gmx-users] Make an index file On 29/04/2012 7:32 PM, Shima Arasteh wrote: Actually, I am confused somehow. I want to equilibrate the system. It contains popc and water. To equilibrate it, using .mdp file I use the nvt.mdp file as below. title = NVT equilibration for POPC define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = POPC SOL ; two coupling groups - more accurate Here you instruct grompp to expect the POPC group... tau_t = 0.1 0.1 ; time constant, in ps ref_t = 323 323 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 323 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed I enter this command: # grompp -f nvt.mdp -c em.gro -p popc.top -o nvt.tpr Getting this fatal error: Group POPC not found in index file. Group names must match either [moleculetype] names or custom index group names,in which case you must supply an index file to the '-n' option of grompp. I don't need index file, do I? What is the problem with my .mdp file? ... but POPC is not defined implicitly by your .top+.gro combination, nor explicitly in an index file supplied with grompp -n. AFAIK if your [moleculetype] is named POPC then it is all OK, but maybe the fact that your .gro file has the POPC residues named POP is confusing that mechanism. As you can see with your earlier example with make_ndx, the POP group is defined implicitly by the residue names in your .gro file, so if you use that output index file and reference POP in your .mdp file, all will be good. You might get away without using that index file, but I am not sure about this. Simpler still is to use Water and non-Water as your T-coupling groups, but this will need changing if down the road you need Protein as well (or such). Mark -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder
On 4/29/12 4:46 AM, J B wrote: Is the problem specific to cylinder geometry? Do other settings work? Does it make a difference if you set values for pull_r0 and pull_r1? -Justin I would think that it is the cylinder geometry that creates the problem. If I use pull = umbrella pull_geometry = distance pull_dim = N N Y pull_start = yes pull_init1= 0.0 pull_ngroups = 1 pull_group0 = DPPC pull_group1 = drug pull_rate1 = 0.0 The molecules stays in place. But pull_geometry=distance is what I would prefer due to the undulations. Changing pull_r0 and pull_r1 still makes the drug molecule move down towards the membrane... Does the cylinder geometry work if you use pull_start = no and pull_init1 equal to your starting (restraint) distance? I'm just trying to go through all of the iterations of what might be failing. In theory, what you're doing is fine but I'd be interested to know if there was something failing in the input parsing such that pull_start is not being properly applied. The screen output of grompp will also tell you what it believes the restraint distance is. If it prints 0, then there's a problem with input processing. If the problem is reproducible in the latest Gromacs version (4.5.5), please file a bug report on redmine.gromacs.org so that it can be investigated. Please provide .tpr file of the system so that the developers can run what you are trying to do and see. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder
Does the cylinder geometry work if you use pull_start = no and pull_init1 equal to your starting (restraint) distance? I'm just trying to go through all of the iterations of what might be failing. In theory, what you're doing is fine but I'd be interested to know if there was something failing in the input parsing such that pull_start is not being properly applied. The screen output of grompp will also tell you what it believes the restraint distance is. If it prints 0, then there's a problem with input processing. If the problem is reproducible in the latest Gromacs version (4.5.5), please file a bug report on redmine.gromacs.org so that it can be investigated. Please provide .tpr file of the system so that the developers can run what you are trying to do and see. -Justin It works if I set pull_start to the initial distance given by g_dist things work just fine. So this will be the way for now at least. Guess that there could be an error in the inout parsing then. Thanks a lot for your help, really appreciate it. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] RE: ask about SDF
I have sent this email to the gromacs users emailing list. I don't actually use g_spatial as it doesn't do what I want it to, I use the older g_sdf script. So can't comment on the output or really help you with it. What you are doing seems right from a quick look through. From what you have told the script to so, it seems like it has done exactly what you asked it to. But without seeing what the system looks like, how it behaves etc, can't say anything beyond that. When I don't see what I expect, I start with a very simple example, ensure that I what I expect there, then make things gradually more complex. That way you can work out if you are using the script incorrectly or what you expected to see is actually incorrect. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: Ianatul Khoiroh [mailto:ianatul_khoi...@yahoo.com] Sent: Friday, 27 April 2012 6:14 PM To: Dallas Warren Subject: ask about SDF Dear Dr. Dallas Warren, I am sorry for sending you a personal e-mail. FYI, I got your email address from gmx-user mailing list. I am new to Gromacs and I did little stuff already in it for the last two months. Briefly, my system consist of 10 oligomers + 990 of solvents in cubic box. I did 15 ns NPT equilibration and currently I am doing analysis stuff such as RDF, density, viscosity, etc. And now I want to try using g_spatial but I stuck on it. I would like to know if you can help me in this. In Gromacs 4.5.4 manual, they wrote like this: 1. Use make_ndx to create a group containing the atoms around which you want the SDF 2. trjconv -s a.tpr -f a.xtc -o b.xtc -center tric -ur compact -pbc none 3. trjconv -s a.tpr -f b.xtc -o c.xtc -fit rot+trans 4. run g_spatial on the .xtc output of step #3. 5. Load grid.cube into VMD and view as an isosurface I have tried to follow those steps but I coud not get any pretty SDF picture like those I read in many papers. :D This is what I have done following the above mentioned steps: step 1: I have my index file step 2: I choose my oligomers (solute, 10 oligomers) as group for centering and I select system (10 oligomers + 990 solvents) as an output group step 3: Again, I choose solute and choose system as an output step 4: I run g_spatial and select 990 solvents for both calculation and output. It gives me warning to increase nab values, so I increase the nab = 100. I got grid.cube but the size of the file is not that big (the manual says it is around 3 copies of *.xtc file). step 5: I load grid.cube into VMD as an isosurface. I got only a sphere of solvents there on the VMD display I would like to know if you could tell me what principally have I did wrong here I run Gromacs 4.5.5 in Cygwin. I really appreciate your help..Thank you very much. Regards, Ianatul Khoiroh Thermophysical Properties Lab. E2-504 Dept. of Chemical Engineering National Taiwan University of Science and Technology (NTUST) #43 Keelung Road, Sec. 4, Taipei 106, Taiwan R.O.C Phone: +886-2-2733-3141 #7605 E-mail: ianatul_khoi...@yahoo.commailto:ianatul_khoi...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Error in using gromacs for MD simulation
I have posted this to the gromacs users emailing list. No files came through, generally they are stripped off the emails before being posted to the emailing list. Should never send attachments to an emailing list, post them to the internet and put the URLs in the email for people to look at if they want to. People can't comment on what isn't available for them to see. Can't suggest anything more about the error. You simply have to find out why there is a difference between the number of atoms in the .gro file and the number defined by the .top file. If you have checked your .gro and .top files, what did you find? The fact that you still get a warning stating the numbers are different indicates you have still missed something. And if you are following a tutorial, then you have done something different to what the tutorial has told you to do. Incorrectly edited a file, used the wrong, old file in a new step etc. Many ways you may have gone wrong. Is it 1 SOL atom or 1 SOL molecule? Be very careful with your terminology with things like that, can seem the same to someone starting out, but they are very different. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: vineetha mandlik [mailto:vinee2h...@gmail.com] Sent: Saturday, 28 April 2012 5:30 AM To: Dallas Warren Subject: Regarding your reply in gromacs users forum Respected Sir, I got your reference from the reply that you have given to the question I put up in Gromacs users forum. First of all I would like to thank you for your reply becos nobody seems to answer the question :) even though I had attached our output files too ... Sir there is problem running with our gromacs program. We carry out MD simulation of proteins using gromacs version 4. And in that case the error obtained is number of coordinates in topology and coordinate file is not the same. As mentioned in gromacs tutorial we have edited even the SOL atoms in topology file, added required number of ions too...yet the same error repeats. We have cross checked both our top and gro files also. Somehow we get a difference of 1 SOL atoms extra between the topology and coordinate file and we do not know how to proceed. I would like to ask you if you have any suggestions sir, any commands to vary... Commands followed are from the following tutorial: http://davapc1.bioch.dundee.ac.uk/prodrg/gmx.pdf. Thanking you. Vineetha Junior research fellow, India -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Question about starting Gromacs 4.5.4 parallel runs using mpirun
On Sat, Apr 28, 2012 at 10:22 PM, Andrew DeYoung adeyo...@andrew.cmu.eduwrote: Hi, Typically, I use Gromacs 4.5.5 compiled with automatic threading. As you know, automatic threading is awesome because it allows me to start parallel runs without calling mpirun. So on version 4.5.5, I can start a job on eight CPUs using simply the command: mdrun -s topol.tpr -nt 8 However, now I am using a different node on my department's cluster, and this node instead has Gromacs 4.5.4 (compiled without automatic threading). So, I must use mpirun to start parallel runs. I have tried this command: mpirun -machinefile mymachines -np 8 mdrun -s topol.tpr I suppose this mdrun executable is not mpi-enabled. Have you compiled mdrun with --enable-mpi option? -Anirban where mymachines is an (extensionless) file containing only the text c60 slots=8. (c60 is the name of the node that I am using.) I get this error message: Missing: program name. Program mdrun either does not exist, is not executable, or is an erroneous argument to mpirun. This is strange, because mdrun is, I think, in my path. For example, if I type mdrun -h, I get the manual page for mdrun (version 4.5.4). Then I tried the command which mdrun, and it gave me this output: /usr/local/gromacs/bin/mdrun So, next I tried to call mdrun via mpirun using the specific path for mdrun: mpirun -machinefile mymachines -np 8 /usr/local/gromacs/bin/mdrun -s topol.tpr This starts running my simulation, but when I look in top, the simulation is only running on a single CPU; there is only one entry for mdrun in top, and it has only %CPU=100 (not eight different entries for mdrun, nor one entry with %CPU=800). Also, the simulation is going at the speed I would expect for running on a single CPU -- it is very slow, so I am convinced that, as top suggests, mdrun is running on only one CPU. Strangely, my colleagues are able to run jobs in parallel using the exact commands that I described above. So apparently something is wrong with my user ID, although there are no error messages (except the error message about Missing: program name that I described). If you have time, do you have any suggestions for other things that I can try? Do you think that something could be wrong with my bashrc file? Thanks for your time! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Question about starting Gromacs 4.5.4 parallel runs using mpirun
On 30/04/2012 3:38 PM, Anirban Ghosh wrote: On Sat, Apr 28, 2012 at 10:22 PM, Andrew DeYoung adeyo...@andrew.cmu.edu mailto:adeyo...@andrew.cmu.edu wrote: Hi, Typically, I use Gromacs 4.5.5 compiled with automatic threading. As you know, automatic threading is awesome because it allows me to start parallel runs without calling mpirun. So on version 4.5.5, I can start a job on eight CPUs using simply the command: mdrun -s topol.tpr -nt 8 However, now I am using a different node on my department's cluster, and this node instead has Gromacs 4.5.4 (compiled without automatic threading). So, I must use mpirun to start parallel runs. I have tried this command: mpirun -machinefile mymachines -np 8 mdrun -s topol.tpr I suppose this mdrun executable is not mpi-enabled. Have you compiled mdrun with --enable-mpi option? -Anirban where mymachines is an (extensionless) file containing only the text c60 slots=8. (c60 is the name of the node that I am using.) I get this error message: Missing: program name. Program mdrun either does not exist, is not executable, or is an erroneous argument to mpirun. This is strange, because mdrun is, I think, in my path. For example, if I type mdrun -h, I get the manual page for mdrun (version 4.5.4). Then I tried the command which mdrun, and it gave me this output: /usr/local/gromacs/bin/mdrun So, next I tried to call mdrun via mpirun using the specific path for mdrun: mpirun -machinefile mymachines -np 8 /usr/local/gromacs/bin/mdrun -s topol.tpr This starts running my simulation, but when I look in top, the simulation is only running on a single CPU; there is only one entry for mdrun in top, and it has only %CPU=100 (not eight different entries for mdrun, nor one entry with %CPU=800). Also, the simulation is going at the speed I would expect for running on a single CPU -- it is very slow, so I am convinced that, as top suggests, mdrun is running on only one CPU. Strangely, my colleagues are able to run jobs in parallel using the exact commands that I described above. So apparently something is wrong with my user ID, although there are no error messages (except the error message about Missing: program name that I described). If you have time, do you have any suggestions for other things that I can try? Do you think that something could be wrong with my bashrc file? Get a simple MPI test program and prove how you can run it in parallel. Then worry about GROMACS. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
