Re: [gmx-users] GPUs and umbrella sampling

On 7/18/11 Jul 18,5:37 PM, Guido Polles wrote: Hi everybody, I noticed that GPU version of gromacs do not support the pull code, hence i suppose g_wham cannot be used to extract a PMF. I would like to just ask if somebody could suggest or give any hint about the way to do umbrella sampling and

Re: [gmx-users] genconf and bonded interactions

On 07/26/2011 07:02 PM, Justin A. Lemkul wrote: Fabio Affinito wrote: On 07/26/2011 05:06 PM, Justin A. Lemkul wrote: Fabio Affinito wrote: Maybe this is a different issue... but it's ok that after the 99,999th atom the counter restarts from zero? 21374SOL OW9 12.986 9.021 7.036 -0.0

Re: [gmx-users] Single long simulation versus multiple short

Hi Tom, 1 ns sounds far too small to explore the various conformational states of a protein of that size, and even worse if you expect the ligand to find it lowest-energy conformation/position (unless you have placed it where it binds). Perhaps you should consider enhanced sampling techniques like

[gmx-users] understanding the output of REMD

dear all , I am new to ReMD simulations.And i done a trial run of 100 ps for 7 replicas . if i view the log file for output i get something like this for every replica for one of the replica the log file looks like this Replica exchange at step 1000 time 2 Repl 0 <-> 1 dE = 6.793e+02 dpV = 0.0

[gmx-users] How to examine the problem of one atom during EM

Hi, Form the begining to 5 steps, during EM, all exit in atom 8524, how do I check it further? I mean, from which parts to examine? I also switched to double version to run the EM. Step=42296, Dmax= 2.9e-10 nm, Epot= -2.17267e+05 Fmax= 1.49514e+04, atom= 8524 ... Step=42313, Dmax= 2.0e-1

[gmx-users] Re: How to exert different lateral pressure profile of a membrane to study its influence on a protein inserted in the double layer membrane?

KONG Xian wrote: Dear Justin A. Lemkul: Thanks for your rapid reply. Just as you said, the result of my simulation with different xy p_ref values didn’t vary, they are almost the same. I think I need consider some other ways to do what I was mean to do.

Re: [gmx-users] understanding the output of REMD

sreelakshmi ramesh wrote: dear all , I am new to ReMD simulations.And i done a trial run of 100 ps for 7 replicas . if i view the log file for output i get something like this for every replica for one of the replica the log file looks like this Replica exchange at step 1000 time 2 Repl 0 <

Re: [gmx-users] How to examine the problem of one atom during EM

lina wrote: Hi, Form the begining to 5 steps, during EM, all exit in atom 8524, how do I check it further? I mean, from which parts to examine? I also switched to double version to run the EM. Open your structure in a visualization program and look at what it might be clashing with.

Re: [gmx-users] genconf and bonded interactions

Fabio Affinito wrote: On 07/26/2011 07:02 PM, Justin A. Lemkul wrote: Fabio Affinito wrote: On 07/26/2011 05:06 PM, Justin A. Lemkul wrote: Fabio Affinito wrote: Maybe this is a different issue... but it's ok that after the 99,999th atom the counter restarts from zero? 21374SOL OW

Re: [gmx-users] How to examine the problem of one atom during EM

On Wed, Jul 27, 2011 at 7:29 PM, Justin A. Lemkul wrote: > > > lina wrote: >> >> Hi, >> >> Form the begining to 5 steps, during EM, all exit in atom 8524, >> how do I check it further? I mean, from which parts to examine? >> I also switched to double version to run the EM. >> > > Open your str

Re: [gmx-users] genconf and bonded interactions

The problem is indeed as I suspected. Your molecules are broken across periodic boundaries in the initial configuration. When you replicate with genbox, you've now replicated broken molecules such that those at the new interfaces between the boxes appear to be intact, but in fact they are no

Re: Re: [gmx-users] How to examine the problem of one atom during EM

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] How to examine the problem of one atom during EM

lina wrote: On Wed, Jul 27, 2011 at 7:29 PM, Justin A. Lemkul wrote: lina wrote: Hi, Form the begining to 5 steps, during EM, all exit in atom 8524, how do I check it further? I mean, from which parts to examine? I also switched to double version to run the EM. Open your structure in

Re: [gmx-users] How to examine the problem of one atom during EM

On Wed, Jul 27, 2011 at 9:06 PM, Justin A. Lemkul wrote: > > > lina wrote: >> >> On Wed, Jul 27, 2011 at 7:29 PM, Justin A. Lemkul wrote: >>> >>> lina wrote: Hi, Form the begining to 5 steps, during EM, all exit in atom 8524, how do I check it further? I mean, from wh

Re: [gmx-users] How to examine the problem of one atom during EM

lina wrote: On Wed, Jul 27, 2011 at 9:06 PM, Justin A. Lemkul wrote: lina wrote: On Wed, Jul 27, 2011 at 7:29 PM, Justin A. Lemkul wrote: lina wrote: Hi, Form the begining to 5 steps, during EM, all exit in atom 8524, how do I check it further? I mean, from which parts to examine? I

Re: [gmx-users] genconf and bonded interactions

Please make sure to keep the discussion on the list. Fabio Affinito wrote: Justin, first of all, I thank you very much for your help: it's very precious. I regret I didn't notice before the molecule was broken. I suggested to you yesterday that your initial configuration was broken. You to

Re: [gmx-users] genconf and bonded interactions

On 07/27/2011 03:38 PM, Justin A. Lemkul wrote: Please make sure to keep the discussion on the list. Sorry, I just was continuing the discussion after sending you my coordinates. Fabio Affinito wrote: Justin, first of all, I thank you very much for your help: it's very precious. I regret

Re: [gmx-users] genconf and bonded interactions

Fabio Affinito wrote: This is the mdrun output: Initializing Domain Decomposition on 4096 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 30.031 nm, LJ-14, atoms 407

Re: [gmx-users] genconf and bonded interactions

On 07/27/2011 03:54 PM, Justin A. Lemkul wrote: Fabio Affinito wrote: This is the mdrun output: Initializing Domain Decomposition on 4096 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bon

Re: [gmx-users] genconf and bonded interactions

Fabio Affinito wrote: On 07/27/2011 03:54 PM, Justin A. Lemkul wrote: Fabio Affinito wrote: This is the mdrun output: Initializing Domain Decomposition on 4096 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-grou

[gmx-users] Extracting .gro file from a crashed run

Hello dear users, I was running a simulation which crashed (without writing output.gro file) Is there a way to extract the .gro file somehow from .trr or any other file? Please guide. Thanks, SN -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-us

Re: [gmx-users] Extracting .gro file from a crashed run

shivangi nangia wrote: Hello dear users, I was running a simulation which crashed (without writing output.gro file) Is there a way to extract the .gro file somehow from .trr or any other file? trjconv -dump To do a restart, there is no need to extract intermediate frames, FYI. See: http

[gmx-users] re: How to exert different lateral pressure profile of a lipid membrane

or your kindly discussion which is inspirational. KONG Xian THU, Beijing __ Information from ESET NOD32 Antivirus, version of virus signature database 6328 (20110727) __ The message was checked by ESET NOD32 Antivirus. http://www.eset.com -- gmx-users mailing listg

Re: [gmx-users] genconf and bonded interactions

On 07/27/2011 04:12 PM, Justin A. Lemkul wrote: Fabio Affinito wrote: On 07/27/2011 03:54 PM, Justin A. Lemkul wrote: Fabio Affinito wrote: This is the mdrun output: Initializing Domain Decomposition on 4096 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (r

Re: [gmx-users] genconf and bonded interactions

Fabio Affinito wrote: This is the key part: processing coordinates... Warning: atom name 18113 in topol.top and out.gro does not match (MN1 - CN1) Warning: atom name 18114 in topol.top and out.gro does not match (MN2 - CN2) Warning: atom name 18115 in topol.top and out.gro does not match (N

Re: [gmx-users] genconf and bonded interactions

Thanks. This actually solved the problem in grompp. I still have problems when running. This is the log of mdrun: Initializing Domain Decomposition on 4096 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances

Re: [gmx-users] genconf and bonded interactions

Fabio Affinito wrote: Thanks. This actually solved the problem in grompp. I still have problems when running. This is the log of mdrun: Initializing Domain Decomposition on 4096 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum int

Re: [gmx-users] genconf and bonded interactions

Ok, the problem is solved. Thank you. Fabio On 07/27/2011 05:17 PM, Justin A. Lemkul wrote: Fabio Affinito wrote: Thanks. This actually solved the problem in grompp. I still have problems when running. This is the log of mdrun: Initializing Domain Decomposition on 4096 nodes Dynamic load bal

[gmx-users] Improving Energy Conservation in NVE Simulation of Water

Hi, I have been simulating 1000 SPC/E water molecules in the NVE ensemble (by using tcoupl = no and pcoupl = no). In these simulations, I am considering only Lennard-Jones interactions; I have "turned charges off" by setting the partial charges on oxygen and hydrogen to zero in a local copy of s

Re: [gmx-users] Improving Energy Conservation in NVE Simulation of Water

Andrew DeYoung wrote: Hi, I have been simulating 1000 SPC/E water molecules in the NVE ensemble (by using tcoupl = no and pcoupl = no). In these simulations, I am considering only Lennard-Jones interactions; I have "turned charges off" by setting the partial charges on oxygen and hydrogen to

[gmx-users] Viscosity units

Dear Gromacs Users, I am trying to learn viscosity calculations using non-equilibrium method in Gromacs 4.5.4. I have gone through Hess paper and several posts on viscosity calculation. I have setup a system of pure water (32000 molecules) and run till 10ns using NPT and setting cos-accelerati

Re: [gmx-users] Viscosity units

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] understanding the output of REMD

after having enough exchanges how to follow the temp trajectory of each replica in REMD ? I tried to make it out from edr file of each replica.looks like replica at a particular temp remains almost at a same temp throughout the simulation and does not visit all the other tempratures.any help please

Re: [gmx-users] understanding the output of REMD

sreelakshmi ramesh wrote: after having enough exchanges how to follow the temp trajectory of each replica in REMD ? I tried to make it out from edr file of each replica.looks like replica at a particular temp remains almost at a same temp throughout the simulation and does not visit all the o

Re: [gmx-users] Re: local pressure v4.5 issues

Hi all, I am trying to figure out a way to port tpr files (which has CHARMM FF) from v4.5 to v4.0.2. This is because i want to use the localpressure calculation which works only in version 4.0.2. When i issue the following command i get grompp_v4.0.2_lp -v -c traj0.gro -o npt_4.0 -p system.top -

Re: [gmx-users] understanding the output of REMD

demultiplex script was used to gave one log file of one replica as the input like perl demux.pl md0.log it gave two output files. replica_index.xvg and replica_temp.xvg. the file replica_temp looks like this 0 01234567 2 012345

Re: [gmx-users] understanding the output of REMD

sreelakshmi ramesh wrote: demultiplex script was used to gave one log file of one replica as the input like perl demux.pl md0.log it gave two output files. |replica_index.xvg| and replica_temp.xvg. the file replica_temp looks like this 0 01234

[gmx-users] disulfide bond, molecule type

Hi, I'm trying to heat a protein. There are two chains, A-chain and B-chain. Two disulfide bonds are between A-chain and B-chain. As I know, I should let A-chain and B-chain belong to the same [molecule type] in .top file if I want to have the two inter-bonds. So, I delete the TER line between

Re: [gmx-users] disulfide bond, molecule type

Hsin-Lin Chiang wrote: Hi, I'm trying to heat a protein. There are two chains, A-chain and B-chain. Two disulfide bonds are between A-chain and B-chain. As I know, I should let A-chain and B-chain belong to the same [molecule type] in .top file if I want to have the two inter-bonds. So, I d

[gmx-users] disulfide bond, molecule type

Hsin-Lin Chiang wrote: >/ Hi, />/ />/ I'm trying to heat a protein. />/ There are two chains, A-chain and B-chain. />/ Two disulfide bonds are between A-chain and B-chain. />/ As I know, I should let A-chain and B-chain belong to the same [molecule />/ type] in .top file if I want to have th

Re: [gmx-users] disulfide bond, molecule type

Hsin-Lin Chiang wrote: Hsin-Lin Chiang wrote: >/ Hi, />/ />/ I'm trying to heat a protein. />/ There are two chains, A-chain and B-chain. />/ Two disulfide bonds are between A-chain and B-chain. />/ As I know, I should let A-chain and B-chain belong to the same [molecule />/ type] in .top

[gmx-users] disulfide bond, molecule type

If you have heated your system severely, you may have generated an unstable system that is on the verge of crashing. VMD seems to allude to some weird geometry and PyMOL would seem to confirm that. I don't know why Rasmol appears OK. If you've somehow "lost" residues then they probably have inf

Re: [gmx-users] disulfide bond, molecule type

Hsin-Lin Chiang wrote: If you have heated your system severely, you may have generated an unstable system that is on the verge of crashing. VMD seems to allude to some weird geometry and PyMOL would seem to confirm that. I don't know why Rasmol appears OK. If you've somehow "lost" residue

[gmx-users] disulfide bond, molecule type

I doubt the chain identifiers are relevant. Both .gro and .pdb files should display properly. The only odd instance I can think of is that without separate chains, some programs may interpret the protein coordinates as a single molecule, but I would think that would only happen in the rarest of